bluuebunny/crossref_metadata_2025 huggingface dataset:
Function Is More Reliable than Quantity to Follow Up the Humoral Response to the Receptor-Binding Domain of SARS-CoV-2-Spike Protein after Natural Infection or COVID-19 Vaccination
Authors: Sariol Carlos , Pantoja Petraleigh , Serrano-Collazo Crisanta , Rosa-Arocho Tiffany , Armina-Rodríguez Albersy , Cruz Lorna , Stone E. , Arana Teresa , Climent Consuelo , Latoni Gerardo , Atehortua Dianne , Pabon-Carrero Christina , Pinto Amelia , Brien James , Espino Ana
Published: October 2021

Both the SARS-CoV-2 pandemic and emergence of variants of concern have highlighted the need for functional antibody assays to monitor the humoral response over time. Antibodies directed against the spike (S) protein of SARS-CoV-2 are an important component of the neutralizing antibody response. In this work, we report that in a subset of patients—despite a decline in total S-specific antibodies—neutralizing antibody titers remain at a similar level for an average of 98 days in longitudinal sampling of a cohort of 59 Hispanic/Latino patients exposed to SARS-CoV-2. Our data suggest that 100% of seroconverting patients make detectable neutralizing antibody responses which can be quantified by a surrogate viral neutralization test. Examination of sera from ten out of the 59 subjects which received mRNA-based vaccination revealed that both IgG titers and neutralizing activity of sera were higher after vaccination compared to a cohort of 21 SARS-CoV-2 naïve subjects. One dose was sufficient for the induction of a neutralizing antibody, but two doses were necessary to reach 100% surrogate virus neutralization in subjects irrespective of previous SARS-CoV-2 natural infection status. Like the pattern observed after natural infection, the total anti-S antibodies titers declined after the second vaccine dose; however, neutralizing activity remained relatively constant for more than 80 days after the first vaccine dose. Furthermore, our data indicates that—compared with mRNA vaccination—natural infection induces a more robust humoral immune response in unexposed subjects. This work is an important contribution to understanding the natural immune response to the novel coronavirus in a population severely impacted by SARS-CoV-2. Furthermore, by comparing the dynamics of the immune response after the natural infection vs. the vaccination, these findings suggest that functional neutralizing antibody tests are more relevant indicators than the presence or absence of binding antibodies.
Global Prevalence of Adaptive and Prolonged Infections’ Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein
Authors: Lennerstrand Johan , Palanisamy Navaneethan
Published: October 2021

Several vaccines with varying efficacies have been developed and are currently administered globally to minimize the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Despite having an RNA-dependent RNA polymerase with a proofreading activity, new variants of SARS-CoV-2 are on the rise periodically. Some of the mutations in these variants, especially mutations on the spike protein, aid the virus in transmission, infectivity and host immune evasion. Further, these mutations also reduce the effectiveness of some of the current vaccines and monoclonal antibodies (mAbs). In the present study, using the available 984,769 SARS-CoV-2 nucleotide sequences on the NCBI database from the end of 2019 till 28 July 2021, we have estimated the global prevalence of so-called ‘adaptive mutations’ and ‘mutations identified in the prolonged infections’, in the receptor-binding domain (RBD) of the spike (S) protein. Irrespective of the geographical region, in the case of the adaptive mutations, N501Y (48.38%) was found to be the dominant mutation followed by L452R (17.52%), T478K (14.31%), E484K (4.69%), S477N (3.29%), K417T (1.64%), N439K (0.7%) and S494P (0.7%). Other mutations were found to be less prevalent (less than 0.7%). Since the last two months, there has been a massive increase of L452R and T478K mutations (delta variant) in certain areas. In the case of prolonged infections’ mutations (long-term SARS-CoV-2 infections), V483A (0.009%) was found to be dominant followed by Q493R (0.009%), while other mutations were found in less than 0.007% of the studied sequences. The data obtained in this study will aid in the development of better infection control policies, thereby curbing the spread of this virus.
Real-Time Genomic Surveillance during the 2021 Re-Emergence of the Yellow Fever Virus in Rio Grande do Sul State, Brazil
Authors: Andrade Miguel de S. , Campos Fabrício S. , Campos Aline A. S. , Abreu Filipe V. S. , Melo Fernando L. , Sevá Anaiá da P. , Cardoso Jader da C. , Dos Santos Edmilson , Born Lucas C. , Silva Cláudia M. D. da , Müller Nicolas F. D. , Oliveira Cirilo H. de , Silva Alex J. J. da , Simonini-Teixeira Danilo , Bernal-Valle Sofía , Mares-Guia Maria A. M. M. , Albuquerque George R. , Romano Alessandro P. M. , Franco Ana C. , Ribeiro Bergmann M. , Roehe Paulo M. , Almeida Marco A. B. de
Published: October 2021

The 2021 re-emergence of yellow fever in non-human primates in the state of Rio Grande do Sul (RS), southernmost Brazil, resulted in the death of many howler monkeys (genus Alouatta) and led the state to declare a Public Health Emergency of State Importance, despite no human cases reported. In this study, near-complete genomes of yellow fever virus (YFV) recovered from the outbreak were sequenced and examined aiming at a better understanding of the phylogenetic relationships and the spatio-temporal dynamics of the virus distribution. Our results suggest that the most likely sequence of events involved the reintroduction of YFV from the state of São Paulo to RS through the states of Paraná and Santa Catarina, by the end of 2020. These findings reinforce the role of genomic surveillance in determining the pathways of distribution of the virus and in providing references for the implementation of preventive measures for populations in high risk areas.
An Investigation of Culicoides (Diptera: Ceratopogonidae) as Potential Vectors of Medically and Veterinary Important Arboviruses in South Africa
Authors: Snyman Jumari , Venter Gert J. , Venter Marietjie
Published: October 2021

Culicoides-borne viruses such as bluetongue, African horse sickness, and Schmallenberg virus cause major economic burdens due to animal outbreaks in Africa and their emergence in Europe and Asia. However, little is known about the role of Culicoides as vectors for zoonotic arboviruses. In this study, we identify both veterinary and zoonotic arboviruses in pools of Culicoides biting midges in South Africa, during 2012–2017. Midges were collected at six surveillance sites in three provinces and screened for Alphavirs, Flavivirus, Orthobunyavirus, and Phlebovirus genera; equine encephalosis virus (EEV); and Rhaboviridae, by reverse transcription polymerase chain reaction. In total, 66/331 (minimum infection rate (MIR) = 0.4) pools tested positive for one or more arbovirus. Orthobunyaviruses, including Shuni virus (MIR = 0.1) and EEV (MIR = 0.2) were more readily detected, while only 2/66 (MIR = 0.1) Middelburg virus and 4/66 unknown Rhabdoviridae viruses (MIR = 0.0) were detected. This study suggests Culicoides as potential vectors of both veterinary and zoonotic arboviruses detected in disease outbreaks in Africa, which may contribute to the emergence of these viruses to new regions.
Incursion of European Bat Lyssavirus 1 (EBLV-1) in Serotine Bats in the United Kingdom
Authors: Folly Arran J. , Marston Denise A. , Golding Megan , Shukla Shweta , Wilkie Rebekah , Lean Fabian Z. X. , Núñez Alejandro , Worledge Lisa , Aegerter James , Banyard Ashley C. , Fooks Anthony R. , Johnson Nicholas , McElhinney Lorraine M.
Published: October 2021

Lyssaviruses are an important genus of zoonotic viruses which cause the disease rabies. The United Kingdom is free of classical rabies (RABV). However, bat rabies due to European bat lyssavirus 2 (EBLV-2), has been detected in Daubenton’s bats (Myotis daubentonii) in Great Britain since 1996, including a fatal human case in Scotland in 2002. Across Europe, European bat lyssavirus 1 (EBLV-1) is commonly associated with serotine bats (Eptesicus serotinus). Despite the presence of serotine bats across large parts of southern England, EBLV-1 had not previously been detected in this population. However, in 2018, EBLV-1 was detected through passive surveillance in a serotine bat from Dorset, England, using a combination of fluorescent antibody test, reverse transcription-PCR, Sanger sequencing and immunohistochemical analysis. Subsequent EBLV-1 positive serotine bats have been identified in South West England, again through passive surveillance, during 2018, 2019 and 2020. Here, we confirm details of seven cases of EBLV-1 and present similarities in genetic sequence indicating that emergence of EBLV-1 is likely to be recent, potentially associated with the natural movement of bats from the near continent
Xeno-Nucleic Acid (XNA) 2’-Fluoro-Arabino Nucleic Acid (FANA) Aptamers to the Receptor-Binding Domain of SARS-CoV-2 S Protein Block ACE2 Binding
Authors: Alves Ferreira-Bravo Irani , DeStefano Jeffrey J.
Published: October 2021

The causative agent of COVID-19, SARS-CoV-2, gains access to cells through interactions of the receptor-binding domain (RBD) on the viral S protein with angiotensin-converting enzyme 2 (ACE2) on the surface of human host cells. Systematic evolution of ligands by exponential enrichment (SELEX) was used to generate aptamers (nucleic acids selected for high binding affinity to a target) to the RBD made from 2ʹ-fluoro-arabinonucleic acid (FANA). The best selected ~79 nucleotide aptamers bound the RBD (Arg319-Phe541) and the larger S1 domain (Val16-Arg685) of the 1272 amino acid S protein with equilibrium dissociation constants (KD,app) of ~10–20 nM, and binding half-life for the RBD, S1 domain, and full trimeric S protein of 53 ± 18, 76 ± 5, and 127 ± 7 min, respectively. Aptamers inhibited the binding of the RBD to ACE2 in an ELISA assay. Inhibition, on a per weight basis, was similar to neutralizing antibodies that were specific for RBD. Aptamers demonstrated high specificity, binding with about 10-fold lower affinity to the related S1 domain from the original SARS virus, which also binds to ACE2. Overall, FANA aptamers show affinities comparable to previous DNA aptamers to RBD and S1 protein and directly block receptor interactions while using an alternative Xeno-nucleic acid (XNA) platform.
Characterization of Adaptive-like γδ T Cells in Ugandan Infants during Primary Cytomegalovirus Infection
Authors: Tuengel Jessica , Ranchal Sanya , Maslova Alexandra , Aulakh Gurpreet , Papadopoulou Maria , Drissler Sibyl , Cai Bing , Mohsenzadeh-Green Cetare , Soudeyns Hugo , Mostafavi Sara , van den Elzen Peter , Vermijlen David , Cook Laura , Gantt Soren
Published: October 2021

Gamma-delta (γδ) T cells are unconventional T cells that help control cytomegalovirus (CMV) infection in adults. γδ T cells develop early in gestation, and a fetal public γδ T cell receptor (TCR) clonotype is detected in congenital CMV infections. However, age-dependent γδ T cell responses to primary CMV infection are not well-understood. Flow cytometry and TCR sequencing was used to comprehensively characterize γδ T cell responses to CMV infection in a cohort of 32 infants followed prospectively from birth. Peripheral blood γδ T cell frequencies increased during infancy, and were higher among CMV-infected infants relative to uninfected. Clustering analyses revealed associations between CMV infection and activation marker expression on adaptive-like Vδ1 and Vδ3, but not innate-like Vγ9Vδ2 γδ T cell subsets. Frequencies of NKG2C+CD57+ γδ T cells were temporally associated with the quantity of CMV shed in saliva by infants with primary infection. The public γδ TCR clonotype was only detected in CMV-infected infants <120 days old and at lower frequencies than previously described in fetal infections. Our findings support the notion that CMV infection drives age-dependent expansions of specific γδ T cell populations, and provide insight for novel strategies to prevent CMV transmission and disease.
A Multidisciplinary Investigation of the First Chikungunya Virus Outbreak in Matadi in the Democratic Republic of the Congo
Authors: De Weggheleire Anja , Nkuba-Ndaye Antoine , Mbala-Kingebeni Placide , Mariën Joachim , Kindombe-Luzolo Esaie , Ilombe Gillon , Mangala-Sonzi Donatien , Binene-Mbuka Guillaume , De Smet Birgit , Vogt Florian , Selhorst Philippe , Matungala-Pafubel Mathy , Nkawa Frida , Vulu Fabien , Mossoko Mathias , Pukuta-Simbu Elisabeth , Kinganda-Lusamaki Eddy , Van Bortel Wim , Wat’senga-Tezzo Francis , Makiala-Mandanda Sheila , Ahuka-Mundeke Steve
Published: October 2021

Early March 2019, health authorities of Matadi in the Democratic Republic of the Congo alerted a sudden increase in acute fever/arthralgia cases, prompting an outbreak investigation. We collected surveillance data, clinical data, and laboratory specimens from clinical suspects (for CHIKV-PCR/ELISA, malaria RDT), semi-structured interviews with patients/caregivers about perceptions and health seeking behavior, and mosquito sampling (adult/larvae) for CHIKV-PCR and estimation of infestation levels. The investigations confirmed a large CHIKV outbreak that lasted February–June 2019. The total caseload remained unknown due to a lack of systematic surveillance, but one of the two health zones of Matadi notified 2686 suspects. Of the clinical suspects we investigated (n = 220), 83.2% were CHIKV-PCR or IgM positive (acute infection). One patient had an isolated IgG-positive result (while PCR/IgM negative), suggestive of past infection. In total, 15% had acute CHIKV and malaria. Most adult mosquitoes and larvae (>95%) were Aedes albopictus. High infestation levels were noted. CHIKV was detected in 6/11 adult mosquito pools, and in 2/15 of the larvae pools. This latter and the fact that 2/6 of the CHIKV-positive adult pools contained only males suggests transovarial transmission. Interviews revealed that healthcare seeking shifted quickly toward the informal sector and self-medication. Caregivers reported difficulties to differentiate CHIKV, malaria, and other infectious diseases resulting in polypharmacy and high out-of-pocket expenditure. We confirmed a first major CHIKV outbreak in Matadi, with main vector Aedes albopictus. The health sector was ill-prepared for the information, surveillance, and treatment needs for such an explosive outbreak in a CHIKV-naïve population. Better surveillance systems (national level/sentinel sites) and point-of-care diagnostics for arboviruses are needed.
Avian Metapneumovirus Subgroup C Induces Mitochondrial Antiviral Signaling Protein Degradation through the Ubiquitin-Proteasome Pathway
Authors: Hou Lei , Hu Xiaohan , Guo Jinshuo , Quan Rong , Wei Li , Wang Jing , Song Jiangwei , Liu Jue
Published: October 2021

The mitochondrial antiviral signaling (MAVS) protein, a critical adapter, links the upstream recognition of viral RNA to downstream antiviral signal transduction. However, the interaction mechanism between avian metapneumovirus subgroup C (aMPV/C) infection and MAVS remains unclear. Here, we confirmed that aMPV/C infection induced a reduction in MAVS expression in Vero cells in a dose-dependent manner, and active aMPV/C replication was required for MAVS decrease. We also found that the reduction in MAVS occurred at the post-translational level rather than at the transcriptional level. Different inhibitors were used to examine the effect of proteasome or autophagy on the regulation of MAVS. Treatment with a proteasome inhibitor MG132 effectively blocked MAVS degradation. Moreover, we demonstrated that MAVS mainly underwent K48-linked ubiquitination in the presence of MG132 in aMPV/C-infected cells, with amino acids 363, 462, and 501 of MAVS being pivotal sites in the formation of polyubiquitin chains. Finally, E3 ubiquitin ligases for MAVS degradation were screened and identified and RNF5 targeting MAVS at Lysine 363 and 462 was shown to involve in MAVS degradation in aMPV/C-infected Vero cells. Overall, these results reveal the molecular mechanism underlying aMPV/C infection-induced MAVS degradation by the ubiquitin-proteasome pathway.
Genomic Signatures in HPV-Associated Tumors
Authors: Hussain Suleman S. , Lundine Devon , Leeman Jonathan E. , Higginson Daniel S.
Published: October 2021

Papillomaviruses dysregulate the G1/S cell cycle transition in order to promote DNA synthesis in S phase, which is a requirement for viral replication. The human papillomaviruses (HPV) E6 and E7 oncoproteins mediate degradation of the cell cycle regulators p53 and Rb, which are two of the most universally disrupted tumor-suppressor genes in all of cancer. The G1/S checkpoint is activated in normal cells to allow sufficient time for DNA repair in G1 before proceeding to replicate DNA and risk propagating unrepaired errors. The TP53 pathway suppresses a variety of such errors, including translocation, copy number alterations, and aneuploidy, which are thus found in HPV-associated tumors similarly to HPV-negative tumors with other mechanisms of TP53 disruption. However, E6 and E7 maintain a variety of other virus–host interactions that directly disrupt a growing list of other DNA repair and chromatin remodeling factors, implying HPV-specific repair deficiencies. In addition, HPV-associated squamous cell carcinomas tumors clinically respond differently to DNA damaging agents compared to their HPV negative counterparts. The focus of this review is to integrate three categories of observations: (1) pre-clinical understanding as to the effect of HPV on DNA repair, (2) genomic signatures of DNA repair in HPV-associated tumor genomes, and (3) clinical responses of HPV-associated tumors to DNA damaging agents. The goals are to try to explain why HPV-associated tumors respond so well to DNA damaging agents, identify missing pieces, and suggest clinical strategies could be used to further improve treatment of these cancers.
Macrophage Depletion via Clodronate Pretreatment Reduces Transgene Expression from AAV Vectors In Vivo
Authors: Yu Darrick L. , Chow Natalie S. M. , Bridle Byram W. , Wootton Sarah K.
Published: October 2021

Adeno-associated virus is a popular gene delivery vehicle for gene therapy studies. A potential roadblock to widespread clinical adoption is the high vector doses required for efficient transduction in vivo, and the potential for subsequent immune responses that may limit prolonged transgene expression. We hypothesized that the depletion of macrophages via systemic delivery of liposome-encapsulated clodronate would improve transgene expression if given prior to systemic AAV vector administration, as has been shown to be the case with adenoviral vectors. Contrary to our expectations, clodronate liposome pretreatment resulted in significantly reduced transgene expression in the liver and heart, but permitted moderate transduction of the white pulp of the spleen. There was a remarkable localization of transgene expression from the red pulp to the center of the white pulp in clodronate-treated mice compared to untreated mice. Similarly, a greater proportion of transgene expression could be observed in the medulla located in the center of the lymph node in mice treated with clodronate-containing liposomes as compared to untreated mice where transgene expression was localized primarily to the cortex. These results underscore the highly significant role that the immune system plays in influencing the distribution and relative numbers of transduced cells in the context of AAV-mediated gene delivery.
Targeting Tat–TAR RNA Interaction for HIV-1 Inhibition
Authors: Alanazi Awadh , Ivanov Andrey , Kumari Namita , Lin Xionghao , Wang Songping , Kovalskyy Dmytro , Nekhai Sergei
Published: October 2021

The HIV-1 Tat protein interacts with TAR RNA and recruits CDK9/cyclin T1 and other host factors to induce HIV-1 transcription. Thus, Tat–TAR RNA interaction, which is unique for HIV-1, represents an attractive target for anti-HIV-1 therapeutics. To target Tat–TAR RNA interaction, we used a crystal structure of acetylpromazine bound to the bulge of TAR RNA, to dock compounds from the Enamine database containing over two million individual compounds. The docking procedure identified 173 compounds that were further analyzed for the inhibition of HIV-1 infection. The top ten inhibitory compounds with IC50 ≤ 6 µM were selected and the three least toxic compounds, T6780107 (IC50 = 2.97 μM), T0516-4834 (IC50 = 0.2 μM) and T5628834 (IC50 = 3.46 μM), were further tested for HIV-1 transcription inhibition. Only the T0516-4834 compound showed selective inhibition of Tat-induced HIV-1 transcription, whereas the T6780107 compound inhibited equally basal and Tat-induced transcription and the T5628834 compound only inhibited basal HIV-1 transcription. The compounds were tested for the inhibition of translation and showed minimal (<25%) effect. The T0516-4834 compound also showed the strongest inhibition of HIV-1 RNA expression and p24 production in CEM T cells and peripheral blood mononuclear cells infected with HIV-1 IIIB. Of the three compounds, only the T0516-4834 compound significantly disrupted Tat–TAR RNA interaction. Additionally, of the three tested compounds, T5628834 and, to a lesser extent, T0516-4834 disrupted Tat–CDK9/cyclin T1 interaction. None of the three compounds showed significant inhibition of the cellular CDK9 and cyclin T1 levels. In silico modelling showed that the T0516-4834 compound interacted with TAR RNA by binding to the bulge formed by U23, U25, C39, G26,C39 and U40 residues. Taken together, our study identified a novel benzoxazole compound that disrupted Tat–TAR RNA interaction and inhibited Tat-induced transcription and HIV-1 infection, suggesting that this compound might serve as a new lead for anti-HIV-1 therapeutics.
In Vitro Characterization and In Vivo Efficacy Assessment in Galleria mellonella Larvae of Newly Isolated Bacteriophages against Escherichia coli K1
Authors: Antoine Céline , Laforêt Fanny , Blasdel Bob , Fall Abdoulaye , Duprez Jean-Noël , Mainil Jacques , Delcenserie Véronique , Thiry Damien
Published: October 2021

Extra-intestinal Escherichia coli express several virulence factors that increase their ability to colonize and survive in different localizations. The K1 capsular type is involved in several infections, including meningitis, urinary tract, and bloodstream infections. The aims of this work were to isolate, characterize, and assess the in vivo efficacy of phages targeting avian pathogenic E. coli (APEC) O18:K1, which shares many similarities with the human strains responsible for neonatal meningitis. Eleven phages were isolated against APEC O18:K1, and four of them presenting a narrow spectrum targeting E. coli K1 strains were further studied. The newly isolated phages vB_EcoS_K1-ULINTec2 were similar to the Siphoviridae family, and vB_EcoP_K1-ULINTec4, vB_EcoP_K1-ULINTec6, and vB_EcoP_K1-ULINTec7 to the Autographiviridae family. They are capsular type (K1) dependent and present several advantages characteristic of lytic phages, such as a short adsorption time and latent period. vB_EcoP_K1-ULINTec7 is able to target both K1 and K5 strains. This study shows that these phages replicate efficiently, both in vitro and in vivo in the Galleria mellonella model. Phage treatment increases the larvae survival rates, even though none of the phages were able to eliminate the bacterial load.
BAF45b Is Required for Efficient Zika Virus Infection of HAP1 Cells
Authors: Persson B. David , Nord Stefan , Lindqvist Richard , Danskog Katarina , Överby Anna K. , Kohl Alain , Willison Hugh J. , Lenman Annasara , Arnberg Niklas
Published: October 2021

The 2016 Zika virus (ZIKV) epidemic illustrates the impact of flaviviruses as emerging human pathogens. For unknown reasons, ZIKV replicates more efficiently in neural progenitor cells (NPCs) than in postmitotic neurons. Here, we identified host factors used by ZIKV using the NCI-60 library of cell lines and COMPARE analysis, and cross-analyzed this library with two other libraries of host factors with importance for ZIKV infection. We identified BAF45b, a subunit of the BAF (Brg1/Brm-associated factors) protein complexes that regulate differentiation of NPCs to post-mitotic neurons. ZIKV (and other flaviviruses) infected HAP1 cells deficient in expression of BAF45b and other BAF subunits less efficiently than wildtype (WT) HAP1 cells. We concluded that subunits of the BAF complex are important for infection of ZIKV and other flavivirus. Given their function in cell and tissue differentiation, such regulators may be important determinants of tropism and pathogenesis of arthropod-borne flaviviruses.
On-Demand Patient-Specific Phenotype-to-Genotype Ebola Virus Characterization
Authors: Beitzel Brett F. , Radoshitzky Sheli R. , Di Paola Nicholas , Brannan Jennifer M. , Kimmel David , Caviness Katie , Soloveva Veronica , Yu Shuiqing , Postnikova Elena N. , Finch Courtney L. , Liu Hu , Prugar Laura , Bakken Russell , Dye John M. , Kugelman Jeffrey R. , Cunningham James M. , Sanchez-Lockhart Mariano , Kuhn Jens H. , Palacios Gustavo
Published: October 2021

Biosafety, biosecurity, logistical, political, and technical considerations can delay or prevent the wide dissemination of source material containing viable virus from the geographic origin of an outbreak to laboratories involved in developing medical countermeasures (MCMs). However, once virus genome sequence information is available from clinical samples, reverse-genetics systems can be used to generate virus stocks de novo to initiate MCM development. In this study, we developed a reverse-genetics system for natural isolates of Ebola virus (EBOV) variants Makona, Tumba, and Ituri, which have been challenging to obtain. These systems were generated starting solely with in silico genome sequence information and have been used successfully to produce recombinant stocks of each of the viruses for use in MCM testing. The antiviral activity of MCMs targeting viral entry varied depending on the recombinant virus isolate used. Collectively, selecting and synthetically engineering emerging EBOV variants and demonstrating their efficacy against available MCMs will be crucial for answering pressing public health and biosecurity concerns during Ebola disease (EBOD) outbreaks.
The Value of Rapid Antigen Tests for Identifying Carriers of Viable SARS-CoV-2
Authors: Shidlovskaya Elena V. , Kuznetsova Nadezhda A. , Divisenko Elizaveta V. , Nikiforova Maria A. , Siniavin Andrei E. , Ogarkova Daria A. , Shagaev Aleksandr V. , Semashko Maria A. , Tkachuk Artem P. , Burgasova Olga A. , Gushchin Vladimir A.
Published: October 2021

The search for effective methods to detect patients who excrete a viable virus is one of the urgent tasks of modern biomedicine. In the present study, we examined the diagnostic value of two antigen tests, BIOCREDIT COVID-19 Ag (RapiGEN Inc., Anyang, Korea) and SGTI-flex COVID-19 Ag (Sugentech Inc., Cheongju, Korea), for their diagnostic value in identifying patients who excrete viable SARS-CoV-2. As part of the study, we examined samples from 106 patients who had just been admitted to the hospital and who had undergone quantitative RT-PCR and assessment of viability of SARS-CoV-2 using cell culture. Assessment of the tests’ value for detecting samples containing viable virus showed high sensitivity for both tests. Sensitivity was 78.6% (95% CI, from 49.2% to 95.3%) for SGTI-flex COVID-19 Ag and 100% (95% CI, from 76.8% to 100%) for Biocredit COVID-19 Ag. The specificity of rapid tests was significantly higher than that of RT-PCR and was 66.3% (95% CI, from 55.7% to 75.8%) and 67.4% (95% CI, from 56.8% to 76.8%) for SGTI-flex COVID-19 Ag and Biocredit COVID-19 Ag versus 30.4% (95% CI, from 21.3% to 40.9%) obtained for PCR. Thus, for tasks of identifying viable SARS-CoV-2 during screening of conditionally healthy people, as well as monitoring those quarantined, rapid tests show significantly better results.
Turnover of SARS-CoV-2 Lineages Shaped the Pandemic and Enabled the Emergence of New Variants in the State of Rio de Janeiro, Brazil
Authors: Francisco Junior Ronaldo da Silva , Lamarca Alessandra P , de Almeida Luiz G P , Cavalcante Liliane , Machado Douglas Terra , Martins Yasmmin , Brustolini Otávio , Gerber Alexandra L , Guimarães Ana Paula de C , Gonçalves Reinaldo Bellini , Alves Cassia , Mariani Diana , Cruz Thais Felix , de Souza Isabelle Vasconcellos , de Carvalho Erika Martins , Ribeiro Mario Sergio , Carvalho Silvia , da Silva Flávio Dias , Garcia Márcio Henrique de Oliveira , de Souza Leandro Magalhães , da Silva Cristiane Gomes , Ribeiro Caio Luiz Pereira , Cavalcanti Andréa Cony , de Mello Claudia Maria Braga , Struchiner Cláudio J. , Tanuri Amilcar , de Vasconcelos Ana Tereza R
Published: October 2021

In the present study, we provide a retrospective genomic epidemiology analysis of the SARS-CoV-2 pandemic in the state of Rio de Janeiro, Brazil. We gathered publicly available data from GISAID and sequenced 1927 new genomes sampled periodically from March 2021 to June 2021 from 91 out of the 92 cities of the state. Our results showed that the pandemic was characterized by three different phases driven by a successive replacement of lineages. Interestingly, we noticed that viral supercarriers accounted for the overwhelming majority of the circulating virus (>90%) among symptomatic individuals in the state. Moreover, SARS-CoV-2 genomic surveillance also revealed the emergence and spread of two new variants (P.5 and P.1.2), firstly reported in this study. Our findings provided important lessons learned from the different epidemiological aspects of the SARS-CoV-2 dynamic in Rio de Janeiro. Altogether, this might have a strong potential to shape future decisions aiming to improve public health management and understanding mechanisms underlying virus dispersion.
HSV-1 DNA Replication—Coordinated Regulation by Viral and Cellular Factors
Authors: Packard Jessica E. , Dembowski Jill A.
Published: October 2021

DNA replication is an integral step in the herpes simplex virus type 1 (HSV-1) life cycle that is coordinated with the cellular DNA damage response, repair and recombination of the viral genome, and viral gene transcription. HSV-1 encodes its own DNA replication machinery, including an origin binding protein (UL9), single-stranded DNA binding protein (ICP8), DNA polymerase (UL30), processivity factor (UL42), and a helicase/primase complex (UL5/UL8/UL52). In addition, HSV-1 utilizes a combination of accessory viral and cellular factors to coordinate viral DNA replication with other viral and cellular processes. The purpose of this review is to outline the roles of viral and cellular proteins in HSV-1 DNA replication and replication-coupled processes, and to highlight how HSV-1 may modify and adapt cellular proteins to facilitate productive infection.
Multisystem Inflammatory Syndrome Following SARS-CoV-2 Infection in Children: One Year after the Onset of the Pandemic in a High-Incidence Area
Authors: Fabi Marianna , Filice Emanuele , Biagi Carlotta , Andreozzi Laura , Palleri Daniela , Mattesini Bianca Elisa , Rizzello Alessia , Gabrielli Liliana , Ghizzi Chiara , Di Luca Daniela , Caramelli Fabio , De Fanti Alessandro , Lanari Marcello
Published: October 2021

SARS-CoV-2 infection in children can trigger cardiovascular manifestations potentially requiring an intensive treatment and defining a new entity named Multisystem Inflammatory Syndrome in Children (MIS-C), whose features partially overlap with Kawasaki Disease (KD). A cross-sectional study including all diagnoses of MIS-C and KD from April 2020 to May 2021 in our metropolitan area was conducted evaluating clinical, laboratory (including immunological response, cytokines, and markers of myocardial damage), and cardiac (coronary and non-coronary) features at onset of the diseases. Evolution of ventricular dysfunction, valve regurgitations, and coronary lesions was documented. The severity of the disease was also considered based on the need for inotropic support and ICU admission. Twenty-four MIS-C were diagnosed (14 boys, median age 82 months): 13/24 cases (54.17%) presented left ventricular dysfunction, 12/24 (50%) required inotropic support, and 10/24 (41.67%) developed coronary anomalies (CALs). All patients received steroids and IVIG at a median time of 5 days (IQR1:4, IQR3:6.5) from onset of fever and heart function normalized 6 days (IQR1: 5, IQR3: 7) after therapy, while CALs persisted in one. One patient (12.5%) required infliximab because of refractory disease and still presented CALs 18 days after therapy. During the same study period, 15 KD were diagnosed: none had ventricular dysfunction, while 7/15 (46.67%) developed CALs. Three out of 15 patients (20%) still presented CALs 46 days from onset. Compared to KD, MIS-C pts have significantly higher IL8 and similar lymphocytes subpopulations. Despite a more severe presentation and initial cardiac findings compared to KD, the myocardial injury in MIS-C has a rapid response to immunomodulatory treatment (median time 6 days), in terms of ventricular function, valve regurgitations, and troponin. Incidence of CALs is similar at onset, but it tends to regress in most of the cases of MIS-C differently than in KD where CALs persist in up to 40% in the subacute stage after treatment.
Development of Antibodies against HPV-6 and HPV-11 for the Study of Laryngeal Papilloma
Authors: Ikegami Taro , Kise Norimoto , Kinjyo Hidetoshi , Kondo Shunsuke , Suzuki Mikio , Tsukahara Narutoshi , Murakami Akikazu , Kiyuna Asanori , Agena Shinya , Tanaka Katsunori , Hasegawa Narumi , Kawakami Junko , Ganaha Akira , Maeda Hiroyuki , Hirakawa Hitoshi
Published: October 2021

Laryngeal papilloma (LP), which is associated with infection by human papillomavirus (HPV)-6 or -11, displays aggressive growth. The precise molecular mechanism underlying the tumorigenesis of LP has yet to be uncovered. Building on our earlier research into HPV-6, in this study, the viral gene expression of HPV-11 was investigated by quantitative PCR and DNA/RNA in situ hybridization. Additionally, newly developed antibodies against the E4 protein of HPV-6 and HPV-11 were evaluated by immunohistochemistry. The average viral load of HPV-11 in LP was 1.95 ± 0.66 × 105 copies/ng DNA, and 88% of HPV mRNA expression was found to be E4, E5a, and E5b mRNAs. According to RNA in situ hybridization, E4 and E5b mRNAs were expressed from the middle to upper part of the epithelium. E4 immunohistochemistry revealed a wide positive reaction in the upper cell layer in line with E4 mRNA expression. Other head and neck lesions with HPV-11 infection also showed a positive reaction in E4 immunohistochemistry. The distribution pattern of HPV DNA, viral mRNA, and E4 protein in LP with HPV-11 infection was quite similar to that of HPV-6. Therefore, it might be possible to apply these E4-specific antibodies in other functional studies as well as clinical applications, including targeted molecular therapies in patients with HPV-6 and HPV-11 infection.
Serological Humoral Immunity Following Natural Infection of Children with High Burden Gastrointestinal Viruses
Authors: Zweigart Mark R. , Becker-Dreps Sylvia , Bucardo Filemón , González Fredman , Baric Ralph S. , Lindesmith Lisa C.
Published: October 2021

Acute gastroenteritis (AGE) is a major cause of morbidity and mortality worldwide, resulting in an estimated 440,571 deaths of children under age 5 annually. Rotavirus, norovirus, and sapovirus are leading causes of childhood AGE. A successful rotavirus vaccine has reduced rotavirus hospitalizations by more than 50%. Using rotavirus as a guide, elucidating the determinants, breath, and duration of serological antibody immunity to AGE viruses, as well as host genetic factors that define susceptibility is essential for informing development of future vaccines and improving current vaccine candidates. Here, we summarize the current knowledge of disease burden and serological antibody immunity following natural infection to inform further vaccine development for these three high-burden viruses.
The Autophagosomes Containing Dengue Virus Proteins and Full-Length Genomic RNA Are Infectious
Authors: Wu Shan-Ying , Chen Yu-Lun , Lee Ying-Ray , Lin Chiou-Feng , Lan Sheng-Hui , Lan Kai-Ying , Chu Man-Ling , Lin Pei-Wen , Yang Zong-Lin , Chen Yen-Hsu , Wang Wen-Hung , Liu Hsiao-Sheng
Published: October 2021

Autophagic machinery is involved in selective and non-selective recruitment as well as degradation or exocytosis of cargoes, including pathogens. Dengue virus (DENV) infectioninduces autophagy that enhances virus replication and vesicle release to evade immune systemsurveillance. This study reveals that DENV2 induces autophagy in lung and liver cancer cells andshowed that DENV2 capsid, envelope, NS1, NS3, NS4B and host cell proinflammatory high mobilitygroup box 1 (HMGB1) proteins associated with autophagosomes which were purified by gradientcentrifugation. Capsid, NS1 and NS3 proteins showing high colocalization with LC3 protein in thecytoplasm of the infected cells were detected in the purified double-membrane autophagosome byimmunogold labeling under transmission electron microscopy. In DENV infected cells, the levels ofcapsid, envelope, NS1 and HMGB1 proteins are not significantly changed compared to the dramaticaccumulation of LC3-II and p62/SQSTM1 proteins when autophagic degradation was blocked bychloroquine, indicating that these proteins are not regulated by autophagic degradation machinery.We further demonstrated that purified autophagosomes were infectious when co-cultured withuninfected cells. Notably, these infectious autophagosomes contain DENV2 proteins, negativestrandand full-length genomic RNAs, but no viral particles. It is possible that the infectivity ofthe autophagosome originates from the full-length DENV RNA. Moreover, we reveal that DENV2promotes HMGB1 exocytosis partially through secretory autophagy. In conclusion, we are the firstto report that DENV2-induced double-membrane autophagosomes containing viral proteins andfull-length RNAs are infectious and not undergoing autophagic degradation. Our novel findingwarrants further validation of whether these intracellular vesicles undergo exocytosis to becomeinfectious autophagic vesicles.
Feline Calicivirus Virulent Systemic Disease: Clinical Epidemiology, Analysis of Viral Isolates and In Vitro Efficacy of Novel Antivirals in Australian Outbreaks
Authors: Bordicchia Matteo , Fumian Tulio Machado , Van Brussel Kate , Russo Alice G. , Carrai Maura , Le Shi-Jia , Pesavento Patricia A. , Holmes Edward C. , Martella Vito , White Peter , Beatty Julia A. , Shi Mang , Barrs Vanessa R.
Published: October 2021

Feline calicivirus (FCV) causes upper respiratory tract disease (URTD) and sporadic outbreaks of virulent systemic disease (FCV-VSD). The basis for the increased pathogenicity of FCV-VSD viruses is incompletely understood, and antivirals for FCV-VSD have yet to be developed. We investigated the clinicoepidemiology and viral features of three FCV-VSD outbreaks in Australia and evaluated the in vitro efficacy of nitazoxanide (NTZ), 2′-C-methylcytidine (2CMC) and NITD-008 against FCV-VSD viruses. Overall mortality among 23 cases of FCV-VSD was 39%. Metagenomic sequencing identified five genetically distinct FCV lineages within the three outbreaks, all seemingly evolving in situ in Australia. Notably, no mutations that clearly distinguished FCV-URTD from FCV-VSD phenotypes were identified. One FCV-URTD strain likely originated from a recombination event. Analysis of seven amino-acid residues from the hypervariable E region of the capsid in the cultured viruses did not support the contention that properties of these residues can reliably differentiate between the two pathotypes. On plaque reduction assays, dose–response inhibition of FCV-VSD was obtained with all antivirals at low micromolar concentrations; NTZ EC50, 0.4–0.6 µM, TI = 21; 2CMC EC50, 2.7–5.3 µM, TI > 18; NITD-008, 0.5 to 0.9 µM, TI > 111. Investigation of these antivirals for the treatment of FCV-VSD is warranted.
COVID-19 Vaccination in Patients with Myasthenia Gravis: A Single-Center Case Series
Authors: Ruan Zhe , Tang Yonglan , Li Chunhong , Sun Chao , Zhu Ying , Li Zhuyi , Chang Ting
Published: October 2021

In this study, we report the safety of coronavirus disease 2019 (COVID-19) vaccine in patients with myasthenia gravis (MG). Patients who were vaccinated against COVID-19 were included. Demographics, clinical characteristics, medications, and vaccination information were collected. The main observation outcome is the worsening of MG symptoms within 4 weeks following COVID-19 vaccination. A total of 22 patients with MG vaccinated for COVID-19 were included. Ten (45.5%) patients had ocular MG (OMG), and 12 (55.5%) patients had generalized MG (GMG). Six (27.3%) patients were female, and the mean (SD) onset age was 45.4 (11.8) years. Nineteen (86.4%) patients were seropositive for acetylcholine receptors (AChR) antibody. Seven (31.8%) patients underwent thymectomy, and four of them confirmed thymoma pathologically. Twenty-one patients were administrated with inactivated vaccines, and the remaining one was administrated with recombinant subunit vaccine. Twenty (90.9%) patients did not present MG symptom worsening within 4 weeks of COVID-19 vaccination, and two (9.1%) patients reported slight symptom worsening but resolved quickly within a few days. Our findings suggest inactivated COVID-19 vaccines might be safe in MG patients with Myasthenia Gravis Foundation of America (MGFA) classification I to II, supporting the recommendation to promote vaccination for MG patients during the still expanding COVID-19 pandemic.
Persuasive Messages Will Not Increase COVID-19 Vaccine Acceptance: Evidence from a Nationwide Online Experiment
Authors: Kachurka Raman , Krawczyk Michał , Rachubik Joanna
Published: October 2021

Although mass vaccination is the best way out of the pandemic, the share of skeptics is substantial in most countries. Social campaigns can emphasize the many arguments that potentially increase acceptance for vaccines: e.g., that they have been developed, tested, and recommended by doctors and scientists; and that they are safe, effective, and in demand. We verified the effectiveness of such messages in an online experiment conducted in February and March 2021 with a sample of almost six thousand adult Poles, which was nationally representative in terms of key demographic variables. We presented respondents with different sets of information about vaccinating against COVID-19. After reading the information bundle, they indicated whether they would be willing to be vaccinated. We also asked them to justify their answers and indicate who or what might change their opinion. Finally, we elicited a number of individual characteristics and opinions. We found that nearly 45% of the respondents were unwilling to be vaccinated, and none of the popular messages we used was effective in reducing this hesitancy. We also observed a number of significant correlates of vaccination attitudes, with men, older, wealthier, and non-religious individuals, those with higher education, and those trusting science rather than COVID-19 conspiracy theories being more willing to be vaccinated. We discuss important consequences for campaigns aimed at reducing COVID-19 vaccine hesitancy.
Effectiveness of the 13-Valent Pneumococcal Conjugate Vaccine on Invasive Pneumococcal Disease in Greenland
Authors: Nikolova Kristiana Alexandrova , Andersson Mikael , Slotved Hans-Christian , Koch Anders
Published: October 2021

The 13-valent pneumococcal conjugate vaccine (PCV13) was introduced in 2010 to the childhood vaccination program in Greenland. This study aimed to estimate the effectiveness of the PCV13 on the incidence of invasive pneumococcal disease (IPD) in children and in adults in Greenland. IPD cases from the pre-PCV13 period (January 1995–September 2010) were compared with the post-PCV13 period (September 2010–October 2020). Register data were collected from laboratory records, IPD reports, the national registry on admissions, and medical files. A total of 295 IPD cases were identified in the study period. Overall IPD incidence rate (IR) declined from the pre-PCV13 period to the post-PCV13 period (IR 23.3 to 15.3 per 100,000 person years). Overall IPD incidence among children decreased significantly, whereas overall IPD incidence among the elderly increased significantly. During the post-PCV13 period, the incidence of vaccine serotype (VT) IPD decreased in all ages, while the incidence of non-vaccine serotype (NVT) IPD increased. This increase was most substantial among elderly ≥60 years. In conclusion, the PCV13 has reduced incidence rates of IPD in Greenland. However, the increase in NVT IPD among the elderly is noteworthy, and sup-ports continued surveillance of IPD in the population of Greenland.
Review: Vaccines and Vaccination against Lumpy Skin Disease
Authors: Tuppurainen Eeva , Dietze Klaas , Wolff Janika , Bergmann Hannes , Beltran-Alcrudo Daniel , Fahrion Anna , Lamien Charles Euloge , Busch Frank , Sauter-Louis Carola , Conraths Franz J. , De Clercq Kris , Hoffmann Bernd , Knauf Sascha
Published: October 2021

The geographical distribution of lumpy skin disease (LSD), an economically important cattle disease caused by a capripoxvirus, has reached an unprecedented extent. Vaccination is the only way to prevent the spread of the infection in endemic and newly affected regions. Yet, in the event of an outbreak, selection of the best vaccine is a major challenge for veterinary authorities and farmers. Decision makers need sound scientific information to support their decisions and subsequent actions. The available vaccine products vary in terms of quality, efficacy, safety, side effects, and price. The pros and cons of different types of live attenuated and inactivated vaccines, vaccination strategies, and associated risks are discussed. Seroconversion, which typically follows vaccination, places specific demands on the tools and methods used to evaluate the effectiveness of the LSD vaccination campaigns in the field. We aimed to give a comprehensive update on available vaccines and vaccination against LSD, to better prepare affected and at-risk countries to control LSD and ensure the safe trade of cattle.
SARS-CoV-2 Neutralizing Antibody Levels Post COVID-19 Vaccination Based on ELISA Method—A Small Real-World Sample Exploration
Authors: Li Xiaoguang , Liang Chao , Xiao Xiumei
Published: October 2021

This study investigated the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) neutralizing antibodies following inoculation with the coronavirus disease (COVID-19) vaccine. From June to July 2021, 127 participants who had completed COVID-19 vaccination (inactivated SARS-CoV-2 vaccine, 64; CoronaVac, 61; CanSino, 2) were recruited and tested using SARS-CoV-2 neutralizing antibody kits. The positive detection rate (inhibition of neutralizing antibodies ≥ 30%) was calculated and stratified according to population characteristics and inoculation time. The positive rate of neutralizing antibody was 47.22% (17/36) in men and 53.85% (49/91) in women, and 54.55% (24/44) in BMI ≥ 24 and 50.60% (42/83) in BMI < 24. Age was stratified as 20–29, 30–39, 40–49, and ≥50; positive detection rates of SARS-CoV-2 neutralizing antibodies were observed in 60.00% (24/40), 50.00% (21/42), 48.39% (15/31), and 42.86% (6/14), respectively, but with no significant difference (x2 = 1.724, p = 0.632). Among 127 vaccinated participants, 66 (51.97%) were positive. The positive detection rate was 63.93% (39/61) with CoronaVac and 42.19% (27/64) with the inactivated SARS-CoV-2 vaccine (significance x2 = 5.927, p = 0.015). Multivariate analysis revealed a significant difference in vaccination times, with average vaccination weeks in the positive and negative groups of 11.57 ± 6.48 and 17.87 ± 9.17, respectively (t= −4.501, p < 0.001). The positive neutralizing antibody rate was 100.00%, 60.00%, 58.33%, 55.56%, 43.14%, 28.57%, and 0.00% at 2–4, 5–8, 9–12, 13–16,17–20, 21–24, and >24 weeks, respectively (x2 = 18.030, p = 0.006). Neutralizing antibodies were detected after COVID-19 inoculation, with differences relating to inoculation timing. This study provides a reference for vaccine evaluation and follow-up immunization strengthening.