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Intro: Canine parvovirus type 2 (PVC-2), Protoparvovirus genus of the Parvoviridae family, is a worldwide distribution virus that affects the Canidae family. In free-living coyotes (Canis latrans), the presence of the PCV-2a, PCV-2b and PCV-2c subtypes of PVC-2 has been reported, but there are no reports of their presence as a cause of clinical damage. The objective of this study is to report the presence of PVC-2c in an outbreak of mild gastroenteritis in three coyote pups detected in northeastern Mexico Methods: During the fall of 2019, in the suburban area of Monterrey, N.L., 3 affected coyote pups were detected with a mild gastroenteric condition consisting of mild diarrhea with loose stools, vomiting, dehydration, loss of appetite, pale mucous membranes, and low weight. Stool samples were tested for Canine Parvovirus (CPV-2), Canine Coronavirus (CCV) or Giardia antigens with a commercial kit. All samples were positive for CPV-2 and these were subsequently analyzed by PCR and sequencing of the CPV-2 VP2 gene. Using bioinformatics, the VP2 gene sequence data obtained were used to establish phylogenetic relationships with homologous sequences reported in coyotes and CPV-2 vaccines. Finding(s): The genetic sequence of VP2 obtained showed a high homology (98.1 to 100%) with CPV-2c. The sequences obtained from the pups showed 100% homology to each other. The phylogenetic tree showed that the sequences reported in coyotes are grouped in different clades and that the sequence of the VP2 gene of CPV-2c from coyote pups is grouped in a different monophyletic group. Conclusion(s): Information suggests that wild coyotes may not only act as asymptomatic reservoir hosts but may also be clinically affected by PVC-2c. It is necessary to carry out studies to know the effects of the genetic subtypes of PVC-2 in the population of coyotes and other wild canids of northeastern Mexico.Copyright © 2023
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Intro: The spike protein of the SARS-CoV-2 virus targets the human cell receptor of angiotensin-converting enzyme (ACE2), including the myocardium and heart's conduction system. Patients diagnosed with COVID-19 have also been found to exhibit cardiac arrhythmia. Here, a whole-genome sequencing analysis using long-read sequencing was proposed to evaluate the virus genome in a patient who presented with AVNRT as a main presentation of COVID-19. Method(s): The sample was recovered from nasopharyngeal and oropharyngeal swab specimens of a 46-year-old female with no comorbidities who presented with palpitation, and ECG showed typical AVNRT features. The RT-qPCR of SARS- CoV-2 was confirmed positive with a CT-value of 15.82. The total RNAs were extracted and proceeded for RT-qPCR and proceeded with Oxford Nanopore Flongle sequencing. The genomics data of the virus was deposited in GISAID (EPI_ISL_3241561) and further analysed using online bioinformatics tools such as Nextclade CLI 2.3.0. Ethical approval (IREC 2021-080) for the study was obtained from IIUM Research Ethics Committee. Finding(s): Here, we reported a total of 29,775 bp near-complete whole-genome belonging to clade 21J (Delta) of AY.79 lineage (also known as B.1.617.2.79), which formed a dominant variant in Malaysia during the time of sampling. Discussion(s): While a previous study showed an association between Delta variant infection with fulminant myocarditis, the present study reported the benign AVNRT as the main presentation of SARS-CoV-2 infection. Furthermore, we observed the presence of the C3037T mutation previously described in the endomyocardial biopsy of a patient with persistent arrhythmia. Conclusion(s): Even though SARS-CoV-2 targets the respiratory tract, the present study supports the evidence that the ACE2 receptors are present in the heart. In addition, COVID19 is causing more and more damage to heart tissue, and viral transcription has been confirmed on cardiomyocytes. Further functional studies are needed to explore the associated mutations and their relation to cardiac manifestation.Copyright © 2023
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Background: Despite increased social vulnerability and barriers to care, there has been a paucity of data on SARS-CoV-2 incidence among key populations in sub-Saharan Africa. We seek to characterize active infections and define transmission dynamics of SARS-CoV-2 among people who inject drugs (PWID) and their sexual and injecting partners from Nairobi and the coastal region in Kenya. Method(s): This was a nested cross-sectional study of SARS-CoV-2 infection from April to July 2021 within a cohort study of assisted partner services for PWID in Kenya. A total of 1000 PWID and their partners (500 living with and 500 living without HIV) were recruited for SARS-CoV-2 antibody testing, of whom 440 were randomly selected to provide self-collected nasal swabs for real-time PCR testing. Whole genome sequencing (WGS) was completed on a limited subset of samples (N=23) with cycle threshold values 32.0. Phylogenetic tree construction and analysis was performed using the Nextstrain pipeline and compared with publicly available SARS-CoV-2 sequences from GenBank. Result(s): A total of 438 (99.5%) participants provided samples for SARS-CoV-2 PCR testing. Median age was 37 (IQR 32-42);128 (29.2%) were female;and 222 (50.7%) were living with HIV. The overall prevalence of SARS-CoV-2 infection identified by RT-PCR was 86 (19.6%). In univariate analyses, there was no increased relative risk of SARSCoV- 2 infection related to positive HIV status, frequenting an injection den, methadone treatment, unstable housing, report of any high-risk exposure, or having a sexual or injecting partner diagnosed with COVID-19 or who died from COVID-19 or flu-like illness. Eight samples were successfully sequenced via WGS and classified as WHO variants of concern: 3 Delta, 3 Alpha, and 2 Beta. Seven were classified into clades predominantly circulating in Kenya during 2021. Notably, two sequences were identical and matched identically to another Kenyan sequence, which is consistent with, though not indictive of, a transmission linkage. Conclusion(s): Overall, the risk of SARS-CoV-2 infection in this population of PWID and their partners was not significantly associated with risk factors related to injection drug use. At a genomic level, the SARS-CoV-2 strains in this study were consistent with contemporary Kenyan lineages circulating during the time and not unique to PWID. Prevention efforts, therefore, must also focus on marginalized groups for control given the substantial amount of mixing that likely occurs between populations.
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Background: Exposure-response (E-R) models were developed for the primary endpoint of hospitalization or death in COVID-19 patients from the Phase 3 portion of the MOVe-OUT study (Clinicaltrials.gov NCT04577797). Beyond dose, these models can identify other determinants of response, highlight the relationship of virologic response with clinical outcomes, and provide a basis for differential efficacy across trials. Method(s): Logistic regression models were constructed using a multi-step process with influential covariates identified first using placebo arm data only. Subsequently the assessment of drug effect based on drug exposure was determined using placebo and molnupiravir (MOV) arm data. To validate the models, the rate of hospitalization/death was predicted for published studies of COVID-19 treatment. All work was performed using R Version 3.0 or later. Result(s): A total of 1313 participants were included in the E-R analysis, including subjects having received MOV (N=630) and placebo (N=683). Participants with missing baseline RNA or PK were excluded (79 from MOV and 16 from placebo arms). The covariates shown to be significant determinants of response were baseline viral load, baseline disease severity, age, weight, viral clade, and co-morbidities of active cancer and diabetes. Day 5 and Day 10 viral load were identified as strong on-treatment predictors of hospitalization/death, pointing to sustained high viral load as driving negative outcomes. Estimated AUC50 was 19900 nM*hr with bootstrapped 95% C.I. of (9270, 32700). In an external validation exercise based on baseline characteristics, the E-R model predicted the mean (95% CI) placebo hospitalization rates across trials of 9.3% (7.6%, 11.7%) for MOVe-OUT, 7.2% (5.3%, 9.8%) for the nirmatrelvir/ritonavir EPIC-HR trial, and 3.2% (1.9%, 5.5%) for generic MOV trials by Aurobindo and Hetero, consistent with the differing observed placebo rates in these trials. The relative reduction in hospitalization/death rate predicted with MOV treatment (relative to placebo) also varied with the above patient populations. Conclusion(s): Overall, the exposure-response results support the MOV dose of 800 mg Q12H for treatment of COVID-19. The results further support that many clinical characteristics impacted hospitalization rate beyond drug exposures which can vary widely across studies. These characteristics also influenced the magnitude of relative risk reduction achieved by MOV in the MOVe-OUT study.
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Background: Viral dynamics models provide mechanistic insights into viral disease and therapeutic interventions. A detailed, mechanistic model of COVID-19 was developed and fit to data from molnupiravir (MOV) trials to characterize the SARS-CoV-2 viral dynamics in MOV-treated and untreated participants and describe the basis for variation across individuals. Method(s): An Immune-Viral Dynamics Model (IVDM) incorporating mechanisms of viral infection, viral replication, and induced innate and adaptive immune response described the dynamics of viral load (VL) from pooled data from MOV Phase 2 and 3 trials (N=1958). Population approaches were incorporated to estimate variation across individuals and to conduct an extensive covariate analysis. Nineteen parameters in a system of five differential equations described SARS-CoV-2 viral dynamics in humans. Six population parameters were successfully informed through fitting to observed trial data while the remaining parameters were fixed based on literature values or calibrated via sensitivity analysis. Result(s): Final viral dynamics and immune response parameters were all estimated with high certainty and reasonable inter-individual variabilities. The model captured the viral load profiles across a wide range of subpopulations and predicted lymphocyte dynamics without using this data to inform the parameters, suggesting inferred immune response curves from this model were accurate. This mechanistic representation of COVID-19 disease indicated that the processes of cellular infection, viral production, and immune response are in a time-varying, non-equilibrium state throughout the course of infection. MOV mechanism of action was best described as an inhibitory process on the infectivity term with estimated AUC50 of 10.5 muM*hr. Covariates identified included baseline viral load on infectivity and age, baseline disease severity, viral clade, baseline viral load, and diabetes on immune response parameters. Greater variation was identified for immune parameters than viral kinetic parameters. Conclusion(s): These findings show that the variation in the human response (e.g., immune response) is more influential in COVID-19 disease than variations in the virus kinetics. The model indicates that immunocompromised patients (due to HIV, organ transplant, active cancer, immunosuppressive therapies) develop an immune response to SARS-CoV-2, albeit more slowly than in immunocompetent, and MOV is effective in further reducing viral loads in the immunocompromised.
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as a global pandemic due to its high transmissibility and pathogenicity. It is a beta clade zoonotic coron-avirus like severe acute respiratory syndrome coronavirus (SARS-CoV) and middle east respiratory syndrome coronavirus (MERS-CoV). Though no effective medication has been developed against the deadly COVID-19 disease, henceforth old antimicrobial drugs have been repurposed to treat the COVID-19 patients. In this report, a brief account of the used medication and the potential mechanism of antimicrobial drugs against SARS-CoV-2 has been provided. Based on the earlier in-cidences, the antimicrobials are expected to lose the battle against SARS-CoV-2. The vast lacuna in the research and development of vaccines has led to overuse of the already formulated antimicro-bial drugs, which in turn has led to a distressing problem called "Antimicrobial resistance (AMR)". A complete assay of AMR has been given including its cause, mechanism, spread, and conse-quences. The other two interlinked problems, namely environmental deterioration and secondary in-fections, are elaborated. Moreover, to combat the AMR problem, the way forward has been discussed in detail.Copyright © 2021 Bentham Science Publishers.
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BACKGROUND: The goal of this analysis was to investigate the relationship of molnupiravir pharmacokinetics (PK) and clinical outcomes (primary endpoint of hospitalization or death) in patients with COVID-19 in the phase 3 cohort of MOVe-OUT (clinicaltrials.gov NCT04577797).1 METHODS: Logistic regression models were constructed using a multi-step process with influential covariates identified first using placebo arm data only and subsequently assessment of drug effect as a function of exposures evaluated using placebo and MOV arm data. Individual estimates of exposure were derived from population PK modeling of sparse samples collected in all patients. All work was performed using R v3.0 or later. RESULT(S): A total of 1,313 participants were included in the exposure-response (E-R) analysis, including subjects on MOV (N = 630) and placebo (N = 683). Participants with missing PK or baseline RNA were excluded (79 from MOV and 16 from placebo arms). The covariates shown to be significant determinants of response were baseline viral load, baseline disease severity, age, weight, viral clade, active cancer, and diabetic risk factors. An additive AUC-based Emax model with a fixed hill coefficient of 1 best represented exposure-dependency in drug effect. Estimated AUC50 was 19,900 nM*hr with bootstrapped 95% confidence interval of (9,270, 32,700). Patients at 800 mg achieved near maximal response, which was larger than the response projected for 200 or 400 mg. CONCLUSION(S): Overall, the E-R results support the MOV dose of 800 mg Q12H for treatment of COVID-19. Many patient characteristics, beyond drug exposures, impacted the risk of hospitalization or death.
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Objective To analyze the epidemiological and genomic characteristics of COVID-19 cases imported by land in Ruili, and to provide reference for border epidemic prevention and control in Yunnan Province. Methods We collected information about SARS-CoV-2 infected individuals from overseas land in Ruili, Yunnan from July to November, 2021. The epidemiological characteristics were statistically analyzed. The second-generation sequencing platform of Illumina was used to conduct high-through-put sequencing on the selected 40 positive samples and to analyze their genotyping and variation characteristics. Results During the study period,Ruili City reported 796 COVID-19 cases from abroad.The median age of COVID-19 cases was 28.5 years (Interquantile range 10, range 1-85). The gender ratio between men and women was 4.61 : 1, Most of these infected individuals engaged in business services, accounting for 49.75% (396/796) , 95.60% of COVID-19 cases were mild and moderate cases. The sequencing results of 34 cases can be divided into three clades according to Nextstrain typing method, including 24 cases belong to 21A(Delta) clade, 9 cases belong to 21I(Delta) clade and 1 case belongs to 20I (Alpha V1) clade. Conclusions The virus genotypes of the cases in this study were mainly divided into three branches and there were some differences among them, most of which were Delta mutants.We should continue to implement border control measures and continue to monitor the virus mutation of imported cases, so as to evaluate the threat of the mutant strain to the current situation of epidemic prevention and control in Yunnan Province.Copyright © 2023, Publication Centre of Anhui Medical University. All rights reserved.
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Coronaviruses are highly virulent and therefore important human and veterinary pathogens worldwide. This study presents the first natural hierarchical classification of Coronaviridae. We also demonstrate a "one-step” solution to incorporate the principles of binomial (binary) nomenclature into taxonomy of Coronaviridae. We strongly support the complete rejection of the non-taxonomic category "virus” in any future taxonomic study in virology. This will aid future recognition of numerous virus species, particularly in the currently monotypic subgenus Sarbecovirus. Commenting on the nature of SARS-CoV-2, the authors emphasize that no member of the Sarbecovirus clade is an ancestor of this virus, and humans are the only natural known host © 2022, Mathematical Biology and Bioinformatics.All Rights Reserved.
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Background: Current SARS-CoV-2 vaccines rely on protective immunity against early clade SARS-CoV-2 and have resulted in seroconversion in a subset of MS patients receiving immunosuppressive DMTs. However, it is unknown if SARS-CoV-2 spike antibodies afford immunity against emerging variants of concern, such as Delta and Omicron. Objective(s): To determine the binding of spike antibodies to early clade, Delta, and Omicron SARS-CoV-2 in patients with MS receiving different DMTs. Method(s): Spike antibody binding to early clade SARS-CoV-2, Delta and Omicron was assessed by flow cytometry using sera collected from 58 patients one month post second dose and one patient 1 month post third dose. All patients were previously determined to be seropositive against Wuhan (early clade spike). Clinical and demographic information including DMT treatment and vaccination timing was collected. Result(s): 53 patients were seropositive for Wuhan, Delta and Omicron spike antibodies. Wuhan Spike antibody titres were high at one month post second vaccination, whereas Delta and Omicron Spike antibody titres were significantly decreased. We observed a 70% and 93% decrease of in immunoreactivity to Delta and Omicron, respectively. Although ocrelizumab and fingolimod decrease Spike antibody titres after vaccination, they did not affect immunoreactivity to variants, in comparison to other DMTS. Conclusion(s): All 53 patients were able to generate a positive antibody response following vaccination. However, there was an observable decrease in the antibody titres and immunoreactivity to the Delta and Omicron variants, in comparison to Wuhan.
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Background. SARS-CoV-2, a novel and highly pathogenic coronavirus, has caused unprecedented global disruption following its introduction into the human population. Beginning in January 2021, a NJ university invited all students to campus and initiated an asymptomatic testing protocol using weekly to twice-weekly PCR-based detection of human saliva samples. RNA extracted from PCR-positive human saliva samples was sequenced for surveillance purposes. Methods. Positive samples were submitted for RNA-Seq analysis (ARTIC amplicon sequencing protocol, Illumina MiSeq) and analyzed using Nextclade and USHER (comparison data from GISAID). Using sequencing data, the evolution, transmission, and emergence of SARS-CoV-2 variants were monitored over time in the campus community. Using sequencing data from NY, PA, and NJ in combination with University data, we performed an IQ-TREE based phylogenetic analysis. Results. Analyzing sequencing data of 1,011 University positive samples we demonstrate that SARS-CoV-2 variants Delta (B.1.617.2) and Omicron (BA.1 and BA.2) were first to emerge following widespread vaccination and, quickly, became predominant. These trends witnessed on campus preceded those same variants emerging in New Jersey, providing evidence of local campus spread distinct from the state-wide pandemic. The analysis of 2,359 total sequences from NY, PA, and NJ in combination with University data, provided evidence of the SARS-CoV-2 transmission chain on campus evolving from out-of-state (January 2021) to local (January 2022) spread over one year of the virus circulating within the community at large. Upon performing a Ct value analysis of 2,822 Princeton University sequences, no significant differences were discovered between N gene Ct values when grouped by age or vaccination status. However, there were significant differences in Ct values between strains. The Emergence of SARS-CoV-2 Variants at Princeton University This plot represents the emergence of SARS-CoV-2 clades at Princeton University, organized by Nextstrain clade and displayed as a proportion out of one. Dates of sample collection range from January 25, 2021, to March 1, 2022. X-axis represents SARS-CoV-2 sample test date (grouped by month);Y-axis represents the count per day organized by Nextstrain clade. Conclusion. Sequencing of positive SARS-CoV-2 samples from population screening of a highly vaccinated University campus community allowed the detection of emergence of new variants that became predominant on campus irrespective of the circulation of variants in the surrounding area.
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Background. SARS-CoV-2 has caused unprecedented global disruption following its introduction into the human population. Beginning in August 2021, a residential college initiated an asymptomatic testing protocol using PCR-based detection of human saliva samples (Thermofisher, TaqPath SARS-CoV-2 Assay;QuantStudio v1.3). In January 2021 all students were invited to campus and were required to test once or twice weekly in an effort to isolate those positive (cases) as early as possible and minimize transmission. Methods. Cases were contacted within 12 hours by trained clinical staff and interviewed with a standardized questionnaire to determine contacts and exposures. Positive samples were submitted for RNA-Seq analysis (ARTIC amplicon sequencing protocol, Illumina MiSeq) and analyzed using Nextclade and USHER (comparison data from GISAID). Using this sequence data, we monitored the evolution, transmission, and emergence of variants over time in the campus community. Results. In March 2022 a one-week break and the activities preceding it were followed by an outbreak of COVID among campus members. All cases were attributed to the Omicron variant. Based on traditional contact tracing 10 presumed clusters of transmission were identified (34 students). Sequence data from these 34 samples were assembled to identify phylogenetic and molecular patterns of similarity. Several molecular signatures were identified. In a group of 5 cases, all were Omicron BA.2.9;these individuals comprised a clinical cluster of students who had travelled together. Other lineages were BA.2 (N=26), BA.1(N=2), BA.2.12. (N=3), BA.2.3 (N=1) and an Omicron Clade 21M variant that appeared to be a BA.1/BA.2 recombinant (N=2). The BA.2.12 samples were contributed over 2 days;they were found in two different clusters (a social club and an artistic group), demonstrating likely transmission between members. The BA.2 samples were distributed across a wide number of student groups, and while not identical with one another, did not fall into the clusters identified by contact tracing, suggesting endemic transmission across our campus. Conclusion. This analysis demonstrates that molecular analysis of SARS-CoV-2 transmission can supplement and inform the data provided by clinical/epidemiological analysis of cases.
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Genomic epidemiology is a crucial weapon in the public health fight against infectious diseases.Whole- Genome Sequencing (WGS) of SARS-CoV-2 provides critical insight into viral transmission and evolution.Oxford Nanopore Technology (ONT) works by monitoring changes to an electrical current as a strand of nucleic acid passes through a protein nanopore and the resulting signal from multiple nucleotides is decoded to provide the specific sequence.Illumina sequencing technology, sequencing by synthesis (SBS), detects base-by-base as they are incorporated into growing DNA strands enabling accurate data. In the present study a comparison between ONT performance on MinION and Illumina ISeq was evaluated.Library preparation was performed on 25 SARS-CoV-2-positive specimens collected at Hygiene Laboratory, San Martino Hospital (Genoa, Italy) by COVID panel CE-IVD kit developed at 4Bases and CleanPlex SARS-CoV-2 NGS Panel by Paragon Genomics, respectively to be sequenced on ONT MinION MK1B and Illumina iSeq100 platforms.Data analysis was carried out using the 4eVAR (4Bases) and Sophia DDM Software (Sophia Genetics) platforms and consensus sequence was analyzed using Nextclade webservice. Each variant was classified according to World Health Organization (WHO), Clade and Lineage.Both technologies correctly identified 7 Delta and 18 Omicron variants. Mean coverage on MinION was 763x, after 3 hours of run, covering 98% of the genome. There was perfect match for the WHO, Clade and the Lineage classification except for one difference along the sub-lineage classification of one omicron variant (BA.2 in MinION, BA.2.3 in Paragon).Single mutations analysis showed 96% overlap on average in mutation classification considering all mutations, 98% considering mutations on Spike protein.The two different technologies show a comparable analytical performance, with small differences concerning precise mutation classification. MinION enables real-time analysis, therefore is faster, cheaper and more flexible than standard sequencing techniques. By this analysis it is confirmed to be a promising platform, with the potential to represent a convenient portable and rapid tool for the SARS-COV2 surveillance.
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Background: COVID-19 vaccination induces protective Spike antibodies. Some responses are attenuated in people with multiple sclerosis (MS) on high efficacy disease-modifying therapies (DMT).Whether antibodies afford immunity against emerging SARS-CoV-2 Variants of Concern (VoC) such as Delta and Omicron is unknown. Aim(s): To assess the longevity and breadth of Spike antibody in MS patients after COVID-19 vaccination. Objective(s): To determine seroconversion and antibody binding toVoC Spike. Method(s): Spike antibodies to Clade A SARS-CoV-2 were assessed in 535 MS sera at baseline (n=292), 1 (n=141) and 6 month (n=67) post-second dose, and 1 month post-third dose (n=35), and 489 health worker controls. When known, COVID- 19 vaccines were BNT162b2 (n= 489 controls, n=108 MS patients) and ChAdOx1-S (n=37).Spike antibody binding to VoC Delta and Omicron BA1 was assessed in 68 sera 1 month post-second dose. Demographic and DMT information was available in 269 patients. Result(s): 123/141 sera at 1 month post-second dose, 66/67 at 6 months post-second dose, and 26/35 at 1 month post-third dose were positive for Spike antibodies.Patients who did not seroconvert at 1 and 6 month post-second and 1 month post-third dose (n=28) were treated with ocrelizumab (n=22), cladribine (n=1), fingolimod (n=4), and siponimod (n=1). At 1 month post-second dose, the median and IQR Spike antibody levels were 67,224+/- 101,251 in the seroconverted MS group compared to 145,510+/- 99,669 in controls (n=489). When patient sera were assessed for binding to Clade A Spike, and VoC Delta and Omicron BA1 Spikes, most sera were able to bind the three different Spike antigens (n=61). However, Spike antibody immunoreactivity was decreased by 70% against Delta Spike and 90% for Omicron BA1 Spike compared to the original clade A Spike.As observed for Clade A Spike antibody, DMTs, such as ocrelizumab, fingolimod, and ofatumumab, decreased the antibody binding to Delta and Omicron Spike. Still, the pattern of antibody recognition was similar between the three Spikes and all DMTs analysed, i.e. alemtuzumab, natalizumab, teriflunomide, and interferons. Our data suggest that, irrespectively of DMTs, antibodies generated after vaccination did not bind Spike from recent VoCs to the same extent as the original Spike used in COVID-19 vaccines. Conclusion(s): Some DMTs reduce Spike antibody titres or prevent seroconversion. The sequence of Spike used in the first generation of vaccines may need to be updated for emerging VoC.
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Introduction/ Background: In Senegal, SARS-CoV-2 incidence evolved with three successive epidemic waves. The first wave started on March 2020 with low virus variability whilst the second outbreak started in December was dominated by the Alpha variant. With the third taking place in June 2021, we investigated the involvement of other variants. Methods: During three waves of the pandemic, 163,788 nasopharyngeal swabs have been analysed at the Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formations (IRESSEF). From those, 10,189 positive samples were screened with Seegene Real-time reverse-transcription polymerase chain reaction RT-PCR new variant. From the screened samples, 972 positives were sequenced and 10% of the negatives for detection of new variants. The ARTIC Network methodology with Oxford Nanopore Technologies (ONT) has been used for sequencing. Results: Our data have overall shown that the Senegalese strains are very similar to each other or closely related to other. During the first wave, the most common clade found was 19A (70.27%) and majority of the samples were of the B.1 (54.05) lineage. We noted more diversity during the second wave where clade 20B (40.82%) was more frequent, followed by clade 20A (28.91%), 20I (10.54%). At the level of lineages, we identified variants of interest as B.1.1.7 (10.54%), B.1.525 (6.12%), and B.1.617.2 (0.68%). In the third wave, we observed at the clade level with mainly 21D (47.69%) and 21A (20%). Impact: SARS-CoV-2 diversity may affect the virus's properties, such as it spreads, disease severity, performance of vaccines, tools, or other public health and social measures. Therefore, such tracking of SARS-CoV-2 variants highlight the role some African institutes like IRESSEF surveillance capabilities through real-time sequencing of SARS-CoV-2 genomes in the local context. Conclusion: In Senegal, the SARS-CoV-2 pandemic has disrupted the organization of the health system. IRESSEF contributed to put in place strategies to respond effectively to the expectations of medical authorities by providing them with data on the strains circulating in Senegal at each moment of the epidemic.
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Introduction/ Background: In Senegal, several labs are involved in COVID-19 diagnosis but only a few have the capacity of genomic sequencing, especially in the public sector. The aim of this study was to describe the contribution of a public health laboratory in COVID-19 diagnosis and molecular epidemiology of SARS-COV-2 in Senegal. Methods: From nasopharyngeal swabs collected from COVID- 19 patients, viral RNA was extracted and an RT-PCR was carried out to detect SARS-COV-2 genes using different kits targeting ORF1ab and N genes using Dan-An Gene Co (LTD of Sun-Yat-Sen University) and Sansure Bio Tech Inc or RdRp and N gene with Abbot Real-Time RT-PCR kit. Genomic characterization of SARS-COV-2 strains were carried out on a subset of positive samples collected from the 3 waves by sequenced using MinIon Oxford Nanopore technology. Results: From July 2020 to Sept 2021, 7988 COVID-19 suspected patients or travelers were tested at Laboratoire de Bacteriologie- Virologie (LBV) of Aristide Le Dantec hospital, an University Teaching Hospital. Among them, 964 patients were positive to SARS-COV-2 giving a positivity rate of 12%. Thereafter, 115 (11.9%) were sequenced including 32, 40, and 43 from the first, second, and third waves, respectively. The most detected variants of the first wave were B.1.1.420 (23%). For the second wave, B.1.1.420 (27.5%) and B.1.1.7 (35%) were the most detected. For the third wave, 42 sequences were Delta variant (B.1.617), and one from 19A clade. Impact: The results of this study highlight the need to enlarge the sequencing capacity to laboratories from the public sector in Senegal, especially university teaching hospitals as they may contribute efficiently to COVID -19 response. Conclusion: Despite the low number of positive samples, the LBV through this experience has proven its capacity to contribute to the national response of the COVID-19 pandemic and in genomic characterization of SARSCOV- 2 in the country. It was also a very good opportunity for a technology transfer from IRESSEF and MCR-Gambia.
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Introduction/ Background: The COVID-19 pandemic has caused significant mortality and multiple variants of SARS-CoV-2 have been documented. Delta is the predominant variant around the world. Genomic surveillance can help country to overcome the pandemic by informing/prevention strategies. We aim to determine the dynamic of SARS-CoV-2 in Brazzaville, ROC, between December 2020-July 2021. Methods: Between December 2020 and July 2021, oropharyngeal swabs from symptomatic individuals (n=600) were screened for COVID-19 from different districts of Brazzaville, ROC. RNA was extracted from swabs using the QIAamp Viral RNA Mini Kit (Qiagen, Hilden, Germany) and subjected to RealStar® SARS-CoV-2 real-time PCR targeting the S gene of SARS-CoV-2 (Altona Diagnostics, Hamburg, Germany) was performed in LightCycler® 480 Instrument II (Roche diagnostics, Mannheim, Germany). Found 317 individuals tested positive for COVID-19 and 182 samples that were having Ct <30 were subjected to Next- Generation Sequencing (NGS). Results: The characteristics of the study population from 171 genomes sequenced are as following, the median age of the subjects was 34 years (IQR: 25 to 47) and 67% (115/171) were males. The genomes were assigned to different pangolin lineages. A total of 15 variants were found circulating during the study period. For phylogenetic analysis, variants B.1.544 and B.1 were clustered into a single, and four sister lineages, B.1.214, B.1.214.1, B.214.2 and B.1.214.3, were clustered into a single clade. The B.1.214.2 was the predominant lineage. The VOC lineages B.1.1.7 and B.1.627.2 now have been finding in circulation in the ROC. Impact: The results from the present study indicate that many SARS-COV-2 variants are circulating in the ROC, and the detection of B.1.1.7 and B.1.617.2 variants for the first time in the country is the raised alarm to the health authorities. Conclusion: Many SARS-COV-2 variants are circulating in the ROC, and the detection of B.1.1.7 and B.1.617.2 variants for the first time in the country is the raised alarm to the health authorities. Thus, the spatiotemporal genomic surveillance of SARS-CoV-2 variants contributes to our understanding of viral dynamics.
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FCoV viruses exhibit great genetic diversity, leading to the presence of FIPV-causing variants. Current molecular evolution analysis and genetic variation studies of FCoV in China are predominately focused on gene encoding the spike protein or other structural proteins, while few studies have evaluated genetic variations in nonstructural FCoV genes, which can play an important role in disease pathogenesis. In this study, the gene encoding the open reading frame (ORF) 7b nonstructural FCoV protein of the Chinese Fujian strain FJLY20201 was amplified from the ascitic fluid of a Chinese domestic cat infected with FIPV and compared with ORF 7b from previously published FCoV strains. Multiple sequence alignment revealed that FJLY20201 exhibited high identity with other Chinese FCoV strains. Phylogenetic analyses indicated that the Chinese strains did not differentiate between type I and type II serotypes of FCoV based on S proteins. In addition, they formed clades and differed genetically from strains originating outside China. This study provides the molecular epidemiology data about the ORF 7b genes of FCoV strains in China. Our results show that the identity of ORF 7b genes was closer between the Chinese isolates, and suggest that variation in ORF 7b is more dependent on geographical origin.
ABSTRACT
Background: Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging coronavirus that is endemic in dromedary camels. Kenya's >3 million camels have high seroprevalence of antibodies against MERS-CoV, with scant evidence of human infection, possibly due to a lower zoonotic potential of Clade C viruses, predominantly found in African camels. Methods: Between April 2018-March 2020, we followed camels aged 0-24 months from 33 camel-keeping homesteads within 50Km of Marsabit town through collecting deep nasal swabs and documenting signs of illness in camels every two weeks. Swabs were screened for MERS-CoV by reverse transcriptase (RT)-polymerase chain reaction (PCR) testing and virus isolation performed on PCR positive samples with cycle threshold (CT) <20. Both the isolates and swab samples (CT <30) were subjected to whole genome sequencing. Human camel handlers were also swabbed and screened for symptoms monthly and samples tested for MERS-CoV by RT-PCR. Results: Among 243 calves, 68 illnesses were recorded in 58 camels (53.9%);50/68 (73.5%) of illnesses were recorded in 2019, and 39 (57.3%) were respiratory symptoms (nasal discharge, hyperlacrimation and coughing). A total of 124/4,702 camel swabs (2.6%) from 83 (34.2%) calves in 15 (45.5%) enrolled compounds were positive for MERS-CoV RNA. Cases were detected between May-September 2019 with three infection peaks, a similar period when three (1.1%) human PCR-positive but asymptomatic cases were detected among 262 persons handling these herds. Sequencing of camel specimens revealed a Clade C2 virus with identical 12 nucleotide deletion at the 3' end of OFR3 region and one nucleotide insertion at the 5' region but lacked the signature ORF4b deletions of other Clade C viruses. Interpretation: We found high levels of transmission of distinct Clade C MERS-CoV among camels in Northern Kenya, with likely spillover infection to humans. These findings update our understanding of MERS-CoV epidemiology in this region.
ABSTRACT
Background: Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a zoonotic virus transmitted to humans from infected dromedary camels. Coordinated by The Food and Agriculture Organization (FAO), Ethiopia and Kenya have ongoing MERS-CoV surveillance studies in camels. The 5-year project combines research and capacity development, with the aim to improve understanding of the epidemiology of the virus in camels and contribute to the global efforts to reduce zoonotic transmission of MERS-CoV. Key development outcomes of the project include important contributions to One Health operationalization in Ethiopia and Kenya. Methods: Since 2016, cross-sectional and longitudinal studies have been implemented to address evolving objectives, including virus detection and prevalence estimates, identifying risk factors for exposure, understanding antibody kinetics, and phylogenetic and phenotypic characteristics of circulating virus. Results: Results revealed that over 60% of camels from Kenya and over 70% of camels from Ethiopia demonstrate exposure to MERS-CoV, while viral RNA was detected in 0.23% of camels in Kenya and 1.08% of camels in Ethiopia. Viruses isolated from both countries were genetically grouped in Clade C2 with MERS-CoV strains found elsewhere in Africa. Phenotypic characteristics of these isolates suggest that MERS-CoV circulating in Africa poses a lower zoonotic risk than clades A and B of the virus circulating in the Arabian Peninsula. These findings have contributed to a better understanding of MERS-CoV transmission risks that will ultimately inform policy directions on risk mitigation. Conclusion: The project has contributed towards the establishment of multi-sectoral Emerging Pandemic Threats Technical Working Group (EPT-TWG) and MERSCoV TWG in Ethiopia and Kenya, respectively. With the emergence of COVID-19, future directions of MERS-CoV work will focus on applied research of risk mitigation interventions, and institutional capacity building on surveillance for early detection of mutations and possible genetic recombination of MERS-CoV with other zoonotic coronaviruses.