A2 Virus Research Articles

Variability of VPU protein in HIV-1 sub-subtype A6 in patients with different stages of HIV infection

The aim of the study: to compare the genetic diversity of the Vpu protein in HIV-1 in the people living with HIV (PLWH) with different stages of the disease.Materials and methods. An analysis was carried out of 259 clinical samples of whole blood from HIV-infected patients with no experience of taking antiretroviral therapy, who were observed at the Center for the Prevention and Control of AIDS and Infectious Diseases, Moscow, Russia. The analysis included the following stages: extraction of proviral DNA, amplification of the region of the virus genome containing the vpu gene, sequencing of amplification products, genotyping, comparison of conservation and amino acid substitutions in the Vpu protein sequences in PLWH with different stages of the disease.Results and discussion. In 255 out of 259 (98.4%) clinical samples, a sub-subtype A6 virus variant was identified. The consensus sequence of the Vpu sub-subtype A6 protein was obtained, which contained 81 amino acids. No significant differences in the conservation of Vpu protein sequences were found between HIV-1 variants obtained from patients with different stages of the disease. Amino acid substitution P3A was significantly more common in PLWH with the second stage of HIV infection.Conclusion. The results obtained highlight the issue of the influence of non-structural proteins of HIV-1 on the course of the disease and indicate directions for possible research in the future.

Intra- and inter-subtype HIV diversity between 1994 and 2018 in southern Uganda: a longitudinal population-based study.

There is limited data on human immunodeficiency virus (HIV) evolutionary trends in African populations. We evaluated changes in HIV viral diversity and genetic divergence in southern Uganda over a 24-year period spanning the introduction and scale-up of HIV prevention and treatment programs using HIV sequence and survey data from the Rakai Community Cohort Study, an open longitudinal population-based HIV surveillance cohort. Gag (p24) and env (gp41) HIV data were generated from people living with HIV (PLHIV) in 31 inland semi-urban trading and agrarian communities (1994-2018) and four hyperendemic Lake Victoria fishing communities (2011-2018) under continuous surveillance. HIV subtype was assigned using the Recombination Identification Program with phylogenetic confirmation. Inter-subtype diversity was evaluated using the Shannon diversity index, and intra-subtype diversity with the nucleotide diversity and pairwise TN93 genetic distance. Genetic divergence was measured using root-to-tip distance and pairwise TN93 genetic distance analyses. Demographic history of HIV was inferred using a coalescent-based Bayesian Skygrid model. Evolutionary dynamics were assessed among demographic and behavioral population subgroups, including by migration status. 9931 HIV sequences were available from 4999 PLHIV, including 3060 and 1939 persons residing in inland and fishing communities, respectively. In inland communities, subtype A1 viruses proportionately increased from 14.3% in 1995 to 25.9% in 2017 (P < .001), while those of subtype D declined from 73.2% in 1995 to 28.2% in 2017 (P < .001). The proportion of viruses classified as recombinants significantly increased by nearly four-fold from 12.2% in 1995 to 44.8% in 2017. Inter-subtype HIV diversity has generally increased. While intra-subtype p24 genetic diversity and divergence leveled off after 2014, intra-subtype gp41 diversity, effective population size, and divergence increased through 2017. Intra- and inter-subtype viral diversity increased across all demographic and behavioral population subgroups, including among individuals with no recent migration history or extra-community sexual partners. This study provides insights into population-level HIV evolutionary dynamics following the scale-up of HIV prevention and treatment programs. Continued molecular surveillance may provide a better understanding of the dynamics driving population HIV evolution and yield important insights for epidemic control and vaccine development.

Complete genome sequence analysis of Reticuloendotheliosis virus integrated in nonhomologous Avipoxvirus

Integration of nucleic acid sequences of Reticuloendotheliosis virus (REV) in Avipoxvirus（APV） has become commonplace. In this study, 4 strains of suspected Fowlpox virus (FPV) and 1 strain of suspected Pigeonpox virus (PPV) collected in Taiyuan, Shanxi Province were cultured in chicken embryos, and the 4b core protein gene was amplified by PCR, and the identity and genome similarity were determined by sequence analysis. The sequences between the end of ORF201 and the beginning of ORF203 of FPV and PPV were then amplified, sequenced, and subjected to sequence comparison to determine genome similarity. The results showed that the isolates were 4 strains of FPV and 1 strain of PPV. The 4 isolated strains of FPV belong to type A1 virus, with 100 % identity to each other and to the FWPV-09-Jilin strain isolated in Jilin, China, and the lowest identity to the type B2 virus TNPV5/NZL/2009, which is only 74 %. PPV belongs to type A2 virus, and its identity with local strain of fowlpox virus was 90.1 %, with the highest identity of 100 % with PPLH and ROPI/W370/ON/2012 and ow_2017_3 strains, which also belong to type A2 pigeonpox virus, and the lowest identity of 73.7 % with TNPV5/NZL/2009, a type B2 virus. The complete genome of REV sequences integrated into FPV and PPV were amplified, and 5 REV nucleic acid sequences were obtained after sequencing and concatenation, with lengths ranging from 7942 to 8005 bp. The identity analysis results indicate that it has high identity with isolates from Northeast China, Guangdong, and Guangxi regions in China. Based on its gp90 protein gene, the REV integrated into the poxvirus belong to type III, with the highest identity of 99.9% with strains such as APC-566 and CY1111, and the lowest identity with REV-Anhui1, at 95.4 %. The length of the pol gene varies among different strains of REV, and its encoded amino acid changes significantly after position 675, with deletions and alterations. This study indicates that all fowlpox viruses isolated in Taiyuan, Shanxi Province have integrated the entire REV gene sequence, with high identity between them. At the same time, it indicates that the pigeonpox virus isolate has also integrated the entire REV gene sequence, and has the highest identity with the integrated REV gene sequence in fowlpox virus.

Effect of human H3N2 influenza virus reassortment on influenza incidence and severity during the 2017–18 influenza season in the USA: a retrospective observational genomic analysis

During the 2017-18 influenza season in the USA, there was a high incidence of influenza illness and mortality. However, no apparent antigenic change was identified in the dominant H3N2 viruses, and the severity of the season could not be solely attributed to a vaccine mismatch. We aimed to investigate whether the altered virus properties resulting from gene reassortment were underlying causes of the increased case number and disease severity associated with the 2017-18 influenza season. Samples included were collected from patients with influenza who were prospectively recruited during the 2016-17 and 2017-18 influenza seasons at the Johns Hopkins Hospital Emergency Departments in Baltimore, MD, USA, as well as from archived samples from Johns Hopkins Health System sites. Among 647 recruited patients with influenza A virus infection, 411 patients with whole-genome sequences were available in the Johns Hopkins Center of Excellence for Influenza Research and Surveillance network during the 2016-17 and 2017-18 seasons. Phylogenetic trees were constructed based on viral whole-genome sequences. Representative viral isolates of the two seasons were characterised in immortalised cell lines and human nasal epithelial cell cultures, and patients' demographic data and clinical outcomes were analysed. Unique H3N2 reassortment events were observed, resulting in two predominant strains in the 2017-18 season: HA clade 3C.2a2 and clade 3C.3a, which had novel gene segment constellations containing gene segments from HA clade 3C.2a1 viruses. The reassortant re3C.2a2 viruses replicated with faster kinetics and to a higher peak titre compared with the parental 3C.2a2 and 3C.2a1 viruses (48 h vs 72 h). Furthermore, patients infected with reassortant 3C.2a2 viruses had higher Influenza Severity Scores than patients infected with the parental 3C.2a2 viruses (median 3·00 [IQR 1·00-4·00] vs 1·50 [1·00-2·00]; p=0·018). Our findings suggest that the increased severity of the 2017-18 influenza season was due in part to twointrasubtypes, cocirculating H3N2 reassortant viruses with fitness advantages over the parental viruses. This information could help inform future vaccine development and public health policies. The Center of Excellence for Influenza Research and Response in the US, National Science and Technology Council, and Chang Gung Memorial Hospital in Taiwan.

A Patinformatics perspective of tomato flu and coxsackie viruses

Tomato flu or tomato fever has been reported to be a viral disease by 'The Lancet Respiratory Medicine' journal, detailing about the first instance of this unexplained sickness which occurred on 6 May 2022. This has spread to few regions of India and viral sequencing in 2022 showed its homology with Coxsackie A16 virus. Tomato flu seemed to be a manifestation of Hand-foot-and-mouth-disease (HFMD) caused by Coxsackie viruses. Patent documents are rich source of technological information in a particular area and patents related to diseases are an important area which when extensively explored may give valid scientific clues. Thus, in the present study, we explored the patent landscape of coxsackie viruses, the causal agent of the tomato flu outbreak, to have far sighted effects in future.

Design of hepadnavirus core protein-based chimeric virus-like particles carrying epitopes from respiratory syncytial virus

Respiratory syncytial virus (RSV) is one of the most important pathogens causing respiratory tract infection in humans, especially in infants and the elderly. The identification and structural resolution of the potent neutralizing epitopes on RSV fusion (F) protein enable an “epitope-focused” vaccine design. However, the display of RSV F epitope II on the surface of the widely-used human hepatitis B virus core antigen (HBcAg) has failed to induce neutralizing antibody response in mice. Here, we used the hepadnavirus core protein (HcAg) from different mammalian hosts as scaffolds to construct chimeric virus-like particles (VLPs) presenting the RSV F epitope II. Mouse immunization showed that different HcAg-based chimeric VLPs elicited significantly different neutralizing antibody responses, among which the HcAg derived from roundleaf bat (RBHcAg) is the most immunogenic. Furthermore, RBHcAg was used as the scaffold platform to present multiple RSV F epitopes, and the immunogenicity was further improved in comparison to that displaying a single epitope II. The designed RBHcAg-based multiple-epitope-presenting VLP formulated with MF59-like adjuvant elicited a potent and balanced Th1/Th2 immune response, and offered substantial protection in mice against the challenge of live RSV A2 virus. The designed chimeric VLPs may serve as the potential starting point for developing epitope-focused vaccines against RSV. Our study also demonstrated that RBHcAg is an effective VLP carrier for presenting foreign epitopes, providing a promising platform for epitope-focused vaccine design.

Kaposi varicelliform eruption: an unusual presentation caused by varicella zoster virus in a healthy adult patient - a case report

BackgroundKaposi Varicelliform Eruptions (KVE), also known as eczema herpeticum, is a rare and potentially life-threatening dermatological condition primarily attributed to herpes simplex virus (HSV) infection, with less frequent involvement of Coxsackie A16, vaccinia, Varicella Zoster, and smallpox viruses. Typically associated with pre-existing skin diseases, especially atopic dermatitis, KVE predominantly affects children but can manifest in healthy adults. Characterized by painful clusters of vesicles and sores on the skin and mucous membranes, it often masquerades as other dermatological disorders. Non-steroidal anti-inflammatory drugs (NSAIDs) are commonly used for pain relief and inflammation, though their potential role as KVE triggers remains uncertain.Case reportHere, we present a case of an 18-year-old female with KVE attributed to Varicella Zoster virus (VZV) and successfully treated with oral acyclovir within a week, underscoring the significance of early recognition and intervention. KVE can manifest with systemic symptoms like fever, fatigue, and lymphadenopathy and may involve multiple organ systems, necessitating possible antibiotic use for complications.ConclusionThis case underscores the importance of prompt KVE identification and consideration of antiviral therapy to enhance patient outcomes. Further research is warranted to elucidate predisposing factors for this rare condition.

Течение энтеровирусной инфекции у детей в Краснодарском крае на современном этапе

Objective. To determine the clinical and epidemiologic features of the course of enterovirus infection (EVI) in Krasnodar Krai. Patients and methods. We analyzed the case histories of children who were treated in the State Budgetary Institution "SKDIB" of Krasnodar from January 2020 to November 2023. For the period from 01.01.2020 to 30.06.2022, out of 1560 patients with suspected acute infectious pathology, EVI was detected in 98 children, of whom boys accounted for 59.2% (n = 58), girls – 40.8% (n = 40). After removal of restrictions on new coronavirus infection from 01.07.2022 to November 2023, EVI was detected in 366 out of 2607 examined patients, of which boys accounted for 55.3% (n = 202), girls – 44.7% (n = 164). Most children (231, 63.1%) came from organized groups. In all forms of EVI, nasopharyngeal swabs, feces, and vesicle contents were examined by polymerase chain reaction; enterovirus RNA was detected in all patients. Molecular typing of enteroviruses was performed in the Federal Budgetary Institution "Center of Hygiene and Epidemiology in Krasnodar Krai". Results. It was revealed that exanthem and neurological forms prevailed during the given periods of observation.Of neurological lesions of EVI, enteroviral meningitis remains the leading form, which as an independent form occurred in 66.9% of cases, in combination with herpangina, exanthema, diarrhea – in 33.1%. The incidence rate of enteroviral meningitis for the period from 07.2022 to 11.2023 is 36.6%, the proportion of encephalitis increased to 2.7%. In the age structure of EVI cases for the period from 01.2020 to 06.2022, the main share was children aged 1 to 3 years old (42, 41.1%), for the period 07.2022–11.2023 – children from 4 to 6 years old (219, 59.9%). Conclusion. All age groups of children were involved in the epidemic process, but children aged 1 to 3 years (45.9%) and 7 to 14 years (22.4%) were sick more often, with the highest number of cases registered in preschool and school educational organizations. The greatest risk of developing severe forms of EVI is observed in children from risk groups. In recent years, there are still risks of epidemic rise in the incidence of exanthem and minor forms of EVI associated with the spread of Coxsackie A6, A16 and other viruses of the Coxsackie A and B species, the probability of spread of enterovirus A71 and possible resumption of circulation of EUNO 30 virus cannot be excluded. Key words: children, enterovirus infection, enteroviral exanthema, enteroviral meningitis, clinic

Hypochlorous acid inactivates oral pathogens and a SARS-CoV-2-surrogate

BackgroundDroplets and aerosols produced during dental procedures are a risk factor for microbial and viral transmission. Unlike sodium hypochlorite, hypochlorous acid (HOCl) is nontoxic to tissues but still exhibits broad microbicidal effect. HOCl solution may be applicable as a supplement to water and/or mouthwash. This study aims to evaluate the effectiveness of HOCl solution on common human oral pathogens and a SARS-CoV-2 surrogate MHV A59 virus, considering the dental practice environment.MethodsHOCl was generated by electrolysis of 3% hydrochloric acid. The effect of HOCl on human oral pathogens, Fusobacterium nucleatum, Prevotella intermedia, Streptococcus intermedius, Parvimonas micra, and MHV A59 virus was studied from four perspectives: concentration; volume; presence of saliva; and storage. HOCl solution in different conditions was utilized in bactericidal and virucidal assays, and the minimum inhibitory volume ratio that is required to completely inhibit the pathogens was determined.ResultsIn the absence of saliva, the minimum inhibitory volume ratio of freshly prepared HOCl solution (45–60 ppm) was 4:1 for bacterial suspensions and 6:1 for viral suspensions. The presence of saliva increased the minimum inhibitory volume ratio to 8:1 and 7:1 for bacteria and viruses, respectively. Applying a higher concentration of HOCl solution (220 or 330 ppm) did not lead to a significant decrease in the minimum inhibitory volume ratio against S. intermedius and P. micra. The minimum inhibitory volume ratio increases in applications of HOCl solution via the dental unit water line. One week of storage of HOCl solution degraded HOCl and increased the minimum growth inhibition volume ratio.ConclusionsHOCl solution (45–60 ppm) is still effective against oral pathogens and SAR-CoV-2 surrogate viruses even in the presence of saliva and after passing through the dental unit water line. This study indicates that the HOCl solution can be used as therapeutic water or mouthwash and may ultimately reduce the risk of airborne infection in dental practice.

МОНИТОРИНГ ЦИРКУЛИРУЮЩИХ НЕПОЛИОМИЕЛИТНЫХ ЭНТЕРОВИРУСОВ КАК ИНСТРУМЕНТ КОНТРОЛЯ И ПРОГНОЗА ЭПИДЕМИОЛОГИЧЕСКОЙ СИТУАЦИИ ПО ЭНТЕРОВИРУСНОЙ ИНФЕКЦИИ В РЕСПУБЛИКЕ БЕЛАРУСЬ

More than 100 serotypes of non-polio enteroviruses (NPEV) that are pathogenic for humans can cause deseases of different manifestations and severity, being a serious health problem in many countries of the world, including the Republic of Belarus. In this regard, monitoring the causative agents of enterovirus infections (EVI) circulating in the country aiming of early new sero- and genotypes detection has much of significance. This work is dedicated to the analysis of NPEV monitoring results concerning their circulation in the territory of the Republic of Belarus in 2021–2022, data on their spectrum, molecular genetics and molecular epidemiological characteristics of the serotypes, as well as on the registered signs of the incidence of EVI. It was found that NPEV that circulated in the country in 2021–2022 were Coxsackie B3, Coxsackie B5, Coxsackie A9, ECHO 7, ECHO 30 and HEV B80 viruses. The group of Coxsackie B viruses prevailed (57,1%) with the dominance of the Coxsackie B3 serotype (35,7%). Coxsackie B5 and ECHO 30 viruses, which have a high epidemic potential, were manifested by genotypes that were actively circulating in the country in the previous years. It is shown that 2022 was the year of the rise in the incidence of EVI. At the time, the prerequisites for sharp NPEV sirculation increase are unlikely though not impossible in case of new sero- or genotypes of NPEV being found.

2321. Long-term immunogenicity of Ad26.RSV.preF/RSV preF protein vaccine against RSV in a phase 2b study by age and risk level

Abstract Background Respiratory syncytial virus (RSV) can cause serious lower respiratory tract disease (LRTD) among older adults. There is no licensed RSV vaccine. In CYPRESS (a randomized, double-blind, placebo-controlled, phase 2b proof-of concept trial; NCT03982199), an Ad26.RSV.preF/RSV preF protein vaccine demonstrated 80.0% efficacy for prevention of RSV LRTD and 69.8% efficacy for prevention of any RSV acute respiratory infection in adults aged ≥65 years through the first RSV season. This study evaluated the durability of immune responses elicited by Ad26.RSV.preF/RSV preF protein after two RSV seasons (up to 1.5 years post-vaccination) in the overall study population and in groups of participants stratified by age and risk level for severe RSV LRTD. Methods Participants (N=5782) were randomized 1:1 to receive vaccine or placebo before the RSV season. The primary endpoint was first occurrence of RSV LRTD. RSV A2 virus neutralizing antibodies (VNAs; through Day 365), RSV preF binding antibodies (through Day 533), and RSV-F–specific IFN-γ enzyme-linked immune absorbent spot (ELISpot; through Day 533), were evaluated in an immunogenicity subset (n=195; ages 65–74 years: n=141; 75–84 years: n=47; ≥85 years: n=6; increased risk [chronic heart or lung disease]: n=48; non-increased risk: n=147). Results In the vaccine group of the immunogenicity subset, RSV A2 VNAs peaked at Day 15 and were maintained at 2.8-fold over baseline at 1 year. Similarly, RSV preF-specific binding antibodies peaked at Day 15 and were maintained at 2.1-fold above baseline at 1.5 years. Median RSV-F–specific IFN-γ T-cell frequency increased from 34 spot-forming cells (SFC)/106 peripheral blood mononuclear cells (PBMCs) at baseline to 143 SFC/106 PBMCs at 1.5 years. Comparable immune responses were observed in age/risk subgroups. No relevant changes were observed in the placebo group at any time point. Pre-existing Ad26 VNAs did not appear to impact RSV-specific immune response durability. Conclusion Ad26.RSV.preF/RSV preF protein vaccine was efficacious and elicited robust, durable (to at least 1.5 years) humoral and cellular immune responses in adults aged ≥65 years, older participants (≥75 years), and in participants with increased risk for severe RSV LRTD. Disclosures Christy A. Comeaux, MD, PhD, Janssen Vaccines &amp; Prevention B.V.: Employee Ann R. Falsey, MD, BioFire Diagnostics: Grant/Research Support|Janssen: Grant/Research Support|Merck Sharp &amp; Dohme: Grant/Research Support|Novavax: Advisor/Consultant|Pfizer: Grant/Research Support Kristi Williams, PhD, Janssen Research and Development: Employee John E. Ervin, MD, The Alliance for Multispecialty Research – KCM: Contractual agreement for conduct of study protocol Arangassery R. Bastian, PhD, Janssen Vaccines &amp; Prevention BV: Employee Joris Menten, PhD, Janssen Infectious Diseases: Employee Els De Paepe, MSc, Janssen Infectious Diseases: employee Sjouke Vandenberghe, PhD, Janssen Infectious Diseases: Employee Eric K. H. Chan, PhD, Janssen Global Services, LLC: Employee Jerald Sadoff, MD, Janssen Vaccines &amp; Prevention BV: Employee Macaya Douoguih, MD, MPH, Janssen Vaccines &amp; Prevention B.V.: Employee Benoit Callendret, PhD, Janssen Vaccines &amp; Prevention B.V.: Employee Esther Heijnen, MD, PhD, Janssen Vaccines &amp; Prevention B.V.: Employee.

Tomato flu-a tell-tale sign of another pandemic or just a benign manifestation of hand foot mouth disease

The world is still dealing with the COVID-19 pandemic, but of a gentle variant. In the midst of the global crisis, in God's own land (Kerala), media highlighted cases of febrile illness similar to flu with red round skin lesions that bear a resemblance to tomatoes that have emerged in children younger than 5 years, known as tomato flu or tomato fever. It could be an aftereffect of chikungunya or dengue, rather than a new viral illness. Numerous reports claim that the tomato flu is truly a viral HFMD variant. Hand, foot, and mouth disease (HFMD) is a common febrile illness characterised by a rash caused by enteroviruses, including Coxsackie A16 (CA16), EV A71, Coxsackie A6, Coxsackie B, and Echo viruses.

Epidemiological Characteristics of Hand, Foot, and Mouth Disease and the Effect of EV71 Vaccination in Chengdu from 2012 to 2020

To analyze the epidemiological characteristics of hand, foot, and mouth disease (HFMD) in Chengdu from 2012 to 2020, to make comparison in order to examine the changes in incidence before and after vaccination was introduced, and to provide basis for the prevention of HFMD in the future. Descriptive epidemiological methods were adopted to analyze the incidence, mortality and rate of severe cases of HFMD cases reported in Chengdu from 2012 to 2020. From 2012 to 2020, the cumulative cases of HFMD reported in Chengdu were as many as 279216, of which, there were 2201 severe cases and 16 deaths. The incidence increased every other year, reaching 326.43 per 100000 person-years, the highest ever, in 2018. The rate of severe cases and mortality had shown a decreasing trend since 2016. A total of 11892 cases of EV71, CoxA16 and other enteroviruses were detected in the laboratory, accounting for 14.8%, 18.8% and 66.3%, respectively. Since 2016, HFMD cases caused by EV71 virus infection had shown an overall decreasing trend, cases caused by Cox A16 virus infection had increased every other year, and cases caused by other enteroviral infections had shown an overall increasing trend. The reported cases were mainly concentrated in children aged 0-5 years (92.1%), with those in the age group of 1-2 years reporting the highest number of cases. For children of different ages, male patients always outnumber female patients. The geographic distribution showed that the areas with high HFMD incidence were always located in the central part of Chengdu City, and the three districts with the highest incidence growth rate were Qingbaijiang District, Shuangliu District, and Longquanyi District. Temporal distribution of HFMD cases showed an obvious bimodal distribution, with most of the cases concentrated in May through August and October through December of each year. The number of new cases reached the highest (12309 cases) in July 2018. While continuing to promote EV71 vaccination in the future, Chengdu also needs to pay more attention to viral infection serotypes other than EV71 and Cox A16 and conduct research on multivalent vaccines against a variety of enteroviruses. The focus of prevention and control can be placed on areas with high population density, large floating populations, large numbers of agriculture-related communities, and insufficient individual awareness of hygiene. For the second circle of Chengdu city, the disinfection of agriculture-related communities should be strengthened, and information sessions or other health education activities could be organized for individuals and daycare facilities with low awareness of the importance of hygiene. In addition, more attention should be given to the prevention and control of HFMD in the high incidence seasons.

Determination of HIV Tropism in Patients with Antiretroviral Therapy Failure in Arkhangelsk Region

The aim of the study was to determine the tropism of the human immunodeficiency virus in patients with virological failure of antiretroviral therapy (ART) from the Arkhangelsk Region based on the analysis of the env gene V3 loop nucleotide sequence.Materials and methods. We used blood plasma samples obtained from 76 HIV-infected persons from the Arkhangelsk Region with virological failure of antiretroviral therapy. The nucleotide sequences of the HIV env gene C2-V3-C3 region were studied by PCR followed by sequencing. The genotype of the studied strains was determined based on the analysis of their phylogenetic relations with reference sequences from the international GenBank database, as well as using specialized programs. To predict viral tropism, the Garrido rule and the online bioinformatic tool Geno2Pheno[coreceptor] were used. The Geno2Pheno[coreceptor] algorithm, determines the false positive rate (FPR) based on the analysis of the env gene V3 loop nucleotide sequence. Results and discussion. Significantly lower representation of R5X4/X4-tropic HIV variants in long-term infected persons with subsubtype A6 virus compared to subtype B virus has been shown. For all FPR cut-off algorithms, a significant correlation between subtype and HIV tropism was observed (p=0.0014 and p=0.013 for FPR 10 % and FPR 20 %, respectively). While among subtype B strains, at least 57 % were identified as R5X4/X4-tropic variants (for an FPR of 10 %), including two strains classified as X4-tropic; among HIV subsubtype A6 even at an FPR of 20 %, the frequency of R5X4/X4-tropic samples only slightly exceeded 22 %. It can be assumed that the dynamics of changes in HIV tropism depends on the virus subtype. Significant differences in the distribution of amino acid residues of the V3 region sequences in the examined group between R5-tropic and R5X4/X4-tropic strains of subsubtype A6 for positions 18 (χ2=7.616, p=0.0058), 21 (χ2=7.281, p=0.007), 24 (χ2=5.587, p=0.0181), and 34 (χ2=5.144, p=0.0233) have been demonstrated. Among the R5X4/X4-tropic strains of the A6 subsubtype, amino acid substitutions were registered at positions 6, 19, 21, 26, 29, 30, which were not found in the R5-tropic A6 strains. The high occurrence frequency of a number of mutations previously described as presumably associated with resistance to maraviroc and similar drugs may indicate a natural polymorphism characteristic of the A6 subsubtype, which does not correlate with resistance to CCR5 co-receptor antagonists.

Evaluating the Breadth of Neutralizing Antibody Responses Elicited by Infectious Bursal Disease Virus Genogroup A1 Strains Using a Novel Chicken B-Cell Rescue System and Neutralization Assay.

Eight infectious bursal disease virus (IBDV) genogroups have been identified based on the sequence of the capsid hypervariable region (HVR) (A1-8). Given reported vaccine failures, there is a need to evaluate the ability of vaccines to neutralize the different genogroups. To address this, we used a reverse genetics system and the chicken B-cell line DT4O to rescue a panel of chimeric IBDVs and perform neutralization assays. Chimeric viruses had the backbone of a lab-adapted strain (PBG98) and the HVRs from diverse field strains: classical F52-70 (A1), US-variant Del-E (A2), Chinese-variant SHG19 (A2), very-virulent UK66l (A3), M04/09 distinct (A4), Italian ITA-04 (A6), and Australian-variant Vic-01/94 (A8). Rescued viruses showed no substitutions at amino-acid positions 253, 284, or 330, previously found to be associated with cell-culture adaptation. Sera from chickens inoculated with wt (F52-70) or vaccine (228E) A1 strains had the highest mean virus neutralization (VN) titers against the Al virus (log2 15.4 and 12.7), and the lowest against A2 viruses (log2 7.4-7.9, p=0.0001- 0.0274), consistent with Al viruses being most antigenically distant from A2 strains, which correlated with the extent of differences in the predicted HVR structure. VN titers against the other genogroups ranged from log2 9.3-13.3, and A1 strains were likely more closely antigenically related to genogroups A3 and A4 than A6 and A8. Our data are consistent with field observations and validate the new method which can used to screen future vaccine candidates for breadth of neutralizing antibodies, and evaluate the antigenic relatedness of different genogroups.

Acral purpura and pityriasis rosea-like eruption following COVID-19 infection

Sir, A 74-year-old female patient treated with angiotensin-converting enzyme inhibitor for arterial hypertension with metformin and atorvastatin for insulin-independent diabetes mellitus and hyperlipidemia, respectively, consulted the outpatient dermatological clinic for a rash that appeared fifteen days prior to consultation. The patient received the second dose of mRNA COVID-19 vaccine on July 29, 2021, and was due to receive the third dose on December 29, yet she fell ill on day 6 of the same month, probably being infected by one of her grandchildren. The eruption consisted of erythematous, purpuric macules on the anterior face of both tibia (Fig. 1a), of a solitary papule on the left hand (Fig. 1b), and of erythematous papules with a scale on the border on the left buttock (Fig. 1c). A collarette formed on the trailing edge of the advancing border of the hand lesion, a clinical sign pathognomonic of pityriasis rosea. Intense pruritus accompanied the eruption. No herald patch was observed, nor lesions on the trunk, being the typical location of lesions of pityriasis rosea, while lesions on the hands are absent in the typical cases of the disease. The oral and genital mucosae were intact. The cutaneous manifestations of COVID-19 include purpuric, chilblain, vesicular, urticarial, and pityriasis rosea-like lesions. Acral lesions are the most frequent location of the cutaneous manifestations associated with COVID-19 infection [1]. An acral distribution of lesions is a feature of mouth, hand, and foot disease due to infection with Coxsackie A16 virus [2], although no reactivation of this virus has been detected during the COVID-19 pandemic, while the reactivation of herpes 6 and herpes 7 virus associated with pityriasis rosea has occurred

Structure-based design of prefusion-stabilized human metapneumovirus fusion proteins

The human metapneumovirus (hMPV) fusion (F) protein is essential for viral entry and is a key target of neutralizing antibodies and vaccine development. The prefusion conformation is thought to be the optimal vaccine antigen, but previously described prefusion F proteins expressed poorly and were not well stabilized. Here, we use structures of hMPV F to guide the design of 42 variants containing stabilizing substitutions. Through combinatorial addition of disulfide bonds, cavity-filling substitutions, and improved electrostatic interactions, we describe a prefusion-stabilized F protein (DS-CavEs2) that expresses at 15 mg/L and has a melting temperature of 71.9 °C. Crystal structures of two prefusion-stabilized hMPV F variants reveal that antigenic surfaces are largely unperturbed. Importantly, immunization of mice with DS-CavEs2 elicits significantly higher neutralizing antibody titers against hMPV A1 and B1 viruses than postfusion F. The improved properties of DS-CavEs2 will advance the development of hMPV vaccines and the isolation of therapeutic antibodies.

Seasonal Pattern of Hand Foot and Mouth Disease in an Out-patient Clinic of a Tertiary Care Pediatric Hospital at Dhaka

Background &amp; Objective: Hand, foot and mouth disease (HFMD) is a contagious disease of children, occurs primarily under five years of age, characterized by a history of brief febrile illness and a typical skin rash over hands and feet with or without sores in mouth, caused usually by Coxsackievirus A16 viruses. It is mainly the disease of tropical and subtropical countries and bears a complex-relation with meteorological variables, like temperature, rainfall and relative humidity, although no study has yet been done in Bangladesh to explain the complex relationship of the disease with these variables. This study sought to describe the occurrence of HFMD and its association with meteorological factors in Dhaka city.&#x0D; Methods: The present cross-sectional study collected data of 231 HFMD cases from the records of the daily register of Out-patient Department of Dhaka Shisu Hospital, Dhaka between January 2018 to December 2019. According to the study protocol a child was identified as having HFMD who had a history of brief febrile illness accompanied by a typical skin rash with or without mouth ulcers. Total number of cases treated monthly at OPD during the period were also recorded. Meteorological data were provided by Bangladesh Meteorological Department, which among others, included monthly average temperature, relative humidity and amount of rainfall. While the outcome variable was monthly number of HFMD cases, the predictive variables were average temperature, humidity and rainfall during the study period.&#x0D; Result: Majority (85.3%) children in the present study was &lt; 5 years old. A male preponderance was observed in the series (60%) with male to ratio being 3:2. A clustering of HFMD cases was observed to occur between June to October when monthly average temperature, total rainfall and humidity all were at their maximum compared to those found between November to April. The clustering of cases was more intense in the year 2019 than that in the year 2018. During the period average monthly temperature was 29.20C, average rainfall was 62.6% (238 mm) of the total annual precipitation and mean relative humidity was 79%. The proportion of HFMD cases out of total cases treated during the period was 2.2% in 2018 and was 4.1% in 2019, which in the dry season (November to April) was 0.4% and 0.5% in 2018 and 2019 respectively.&#x0D; Conclusion: The study concluded that majority of the HFMD cases occur under five years of age and boys are more likely to have the infection than the girls. A seasonality of HFMD occurrence is observed with a higher number of cases occurring in the monsoon season and fewer cases in the dry season. Clustering of HFMD cases occur between May to October when monthly average temperature, total rainfall and humidity all are at peak compared to those in November to April of the year.&#x0D; Ibrahim Card Med J 2021; 11 (1): 14-20

Chitinase 3-like 1 is involved in the induction of IL-8 expression by double-stranded RNA in airway epithelial cells

Viral respiratory infection causes inflammatory lung disease. Chitinase 3-like 1 (CHI3L1) contributes to airway inflammation, but its role in human airway epithelial cells following viral infection is unclear. Thus, we investigated whether CHI3L1 regulates inflammatory responses caused by viral infections in airway epithelial cells. Human bronchial epithelial cells, BEAS-2B, were stimulated with a synthetic analog of viral double-stranded RNA, polyinosinic:polycytidylic acid (poly(I:C)). To confirm the specific role of CHI3L1, CHI3L1 was knocked down in BEAS-2B cells using shRNA lentivirus. The expression of CHI3L1 and proinflammatory cytokines such as IL-8 and phosphorylation of mitogen-activated protein kinase (MAPK) pathways were analyzed. In addition to poly(I:C), BEAS-2B cells were infected with the human respiratory syncytial virus (RSV) A2 strain, and CHI3L1 and IL-8 expression was analyzed. Stimulating the cells with poly(I:C) increased CHI3L1 and IL-8 expression, whereas IL-8 expression was abrogated in CHI3L1 knockdown BEAS-2B cells. Poly(I:C) stimulation of BEAS-2B cells resulted in phosphorylation of MAPK pathways, and inhibition of MAPK pathways significantly abolished IL-8 secretion. Phosphorylation of MAPK pathways was diminished in CHI3L1 knockdown BEAS-2B cells. Infection with RSV increased CHI3L1 and IL-8 expression. IL-8 expression induced by RSV infection was abrogated in CHI3L1 knockdown cells. In conclusion, CHI3L1 may be involved in IL-8 secretion by regulating MAPK pathways during respiratory viral infections in airway epithelial cells.

Stability of SARS-CoV-2 and other airborne viruses under different stress conditions.

Viral stability under stress conditions may directly affect viral dissemination, seasonality, and pathogenesis. We exposed airborne viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), mumps virus, coxsackievirus B5, human rhinovirus A16, and respiratory syncytial virus, to different temperatures, UV light exposure time, pH values, and osmotic pressures and measured the remaining viral infectivity. Reduced thermal stability was observed for coxsackievirus B5 at 45 °C, while SARS-CoV-2 demonstrated residual infectivity at 55 °C. UV light exposure was an efficient means of viral inactivation but was less efficient for non-enveloped viruses. Rhinovirus A16 and respiratory syncytial virus demonstrated extreme sensitivity to acid conditions, while SARS-CoV-2, rhinovirus A16, and respiratory syncytial virus were unstable in an alkaline environment. The information obtained in this study will be useful for the development of viral inactivation methods and may be correlated with epidemiological and seasonal viral characteristics.