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Objectives Human leukocyte antigens (HLA) are highly diverse transmembrane proteins that present viral peptides to T cells and launch pathogen-specific immune responses. We aim to investigate the correlation between HLA evolutionary divergence (HED), a surrogate for the capacity to present different peptides, and the outcomes of SARS-CoV-2 infection in a cohort from the St. Louis Metropolitan area. Methods We enrolled adult patients with SARS-CoV-2 infection confirmed by RT-PCR who were hospitalized at two tertiary hospitals in St. Louis between March and July 2020. Genomic DNA was extracted from peripheral blood and genotyped by next-generation sequencing (NGS). HLA alleles were assigned based on key-exon sequences (G group) and limited to the 2-field resolution. HED was calculated by Grantham distance, which considers the difference in composition, polarity, and molecular volume between each pair of amino acids from maternal and paternal HLA. The HED score was obtained for HLA class I (HLA-A, -B, and -C) genotypes using the HLAdivR package in R. Clinical data were collected retrospectively from electronic medical records. A poor outcome was defined as an admission to the intensive care unit (ICU), a need for mechanical ventilation, or death. A favorable outcome was defined as the absence of the above poor outcomes. Results A total of 234 patients were enrolled in this study, 96 being females (41%). The median age and BMI were 66 years old and 28.30 kg/m2, respectively. African Americans comprised 71.4% of the cohort. Only 19 patients (8.1%) presented with no comorbidity;the rest had one or more comorbidities, with cardiovascular diseases being the most common. A total of 137 (58.5%) patients had poor outcomes from SARS-CoV-2 infection, while 97 (41.5%) patients had a favorable outcome. We detected a significant association between higher HLA-B HED and favorable outcomes, with each 1-point increase in HLA-B HED associated with 8% increased probability for the composite endpoint (OR 1.08, 95% CI=1.01-1.16, P = 0.04). The HED scores calculated for HLA-A or HLA-C were not significantly different between patients with favorable or poor outcomes. In a multivariate logistic regression analysis, increased HLA-B HED score, younger age, and no comorbidity were independently associated with favorable outcomes (P = 0.02, P = 0.01, and P = 0.05, respectively). Conclusion Our study shows a significant correlation between lower HLA-B HED scores and poor outcomes after SARS-CoV-2 infection. This finding suggests that maximizing the presentation of diverse SARS-CoV-2 peptides by HLA-B alleles may improve the clearance of SARS-CoV-2. Further studies are warranted to understand the functional and mechanistic implications of this finding.
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Simple SummaryDuring the long-term co-evolution of the virus and the host, even closely related vaccines may emerge with incomplete protective immunity due to the mutations or deletions of amino acids at specific antigenic sites. The mutation of PEDV was accelerated by the recombination of different strains and the mutation of the strains adapting to the environment. These mutations either cause immune escape from conventional vaccines or affect the virulence of the virus. Therefore, researching and developing new vaccines with cross-protection through continuous monitoring, isolation and sequencing are important to determine whether their genetic characteristics are changed and to evaluate the protective efficacy of current vaccines. The porcine epidemic diarrhea virus (PEDV) can cause severe piglet diarrhea or death in some herds. Genetic recombination and mutation facilitate the continuous evolution of the virus (PEDV), posing a great challenge for the prevention and control of porcine epidemic diarrhea (PED). Disease materials of piglets with PEDV vaccination failure in some areas of Shanxi, Henan and Hebei provinces of China were collected and examined to understand the prevalence and evolutionary characteristics of PEDV in these areas. Forty-seven suspicious disease materials from different litters on different farms were tested by multiplex PCR and screened by hematoxylin-eosin staining and immunohistochemistry. PEDV showed a positivity rate of 42.6%, infecting the small and large intestine and mesenteric lymph node tissues. The isolated strains infected Vero, PK-15 and Marc-145 multihost cells and exhibited low viral titers in all three cell types, as indicated by their growth kinetic curves. Possible putative recombination events in the isolates were identified by RDP4.0 software. Sequencing and phylogenetic analysis showed that compared with the classical vaccine strain, PEDV SX6 contains new insertion and mutations in the S region and belongs to genotype GIIa. Meanwhile, ORF3 has the complete amino acid sequence with aa80 mutated wild strains, compared to vaccine strains CV777, AJ1102, AJ1102-R and LW/L. These results will contribute to the development of new PEDV vaccines based on prevalent wild strains for the prevention and control of PED in China.
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Objective: Epidemiology and genetic variations of the infectious bronchitis virus(IBV) in Fujian province were studied. Method: Two strains of virus isolated from the diseased chickens in Fujian in 2021 were identified by chicken embryo pathogenicity test, electron microscope observation, and RT-PCR. S1 genes of the isolates were cloned, sequenced, and analyzed using biological software. Result: The two IBV strains were code named FJ-NP01 and FJ-FZ01. The full length of S1 of FJ-NP01 was 1 629 nt encoding 543 amino acids, and that of FJ-FZ01, 1 620 nt encoding 540 amino acids. The S1 gene cleavage site of FJ-FZ01 was HRRRR, same as all reference strains of genotype I branch;while that of FJ-NP01 HRRKR differed from the reported site of IBV isolated from genotype IV but same as that of TC07-2 reference strain of genotype VI. The homology of nucleotide and amino acid between the two isolates was 83.2% and 79.6%, respectively, but merely 75.7%-76.3%and 77.1%-83.5% with the Mass-type conventional vaccines H120 and H52, respectively. Further analysis showed that FJ-NP01was from a recombination event between CK CH GD LZ12-4 and L-1148, the homology of nucleotide acid between 1438-1506 nt of FJ-NP01 with CK CH GD LZ12-4 was 97%, and 95.9% between the other nucleotide acid of S1 gene with L-1148. Conclusion: It appeared that the IBV epidemic experienced in the province was complex in nature and that the existing Mass vaccines would not provide sufficient immune protection to deter the spread.
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[Objective] To prepare broad-spectrum monoclonal antibody against N protein of avian infectious bronchitis virus (IBV), so as to lay a foundation for identifying conservative domain epitope of N protein and establish a universal IBV detection method. [Method] N protein of GX-YL5, a representative strain of IBV dominant serotype in Guangxi, was expressed in prokaryote. BALB/c mice were immunized with the purified protein. After the serum titer of the immunized mice reached 104 or more, the splenocytes were fused with SP2/0 myeloma cells. After screening by indirect ELISA, monoclonal antibody was prepared by ascites-induced method. Western blotting, IFA and indirect ELISA were used to identify the titer, subtype, reaction specificity and cross-reaction spectrum. And the prepared monoclonal antibody was used for immunohistochemical detection. And the prepared monoclonal antibody was used to detect the IBV in the trachea and kidney tissues of SPF chickens artificially infected with 4 representative IBV variants (GX-N130048, GX-N160421, GX-QZ171023 and GX-QZ170728). [Result] The prepared monoclonal antibody N2D5 had a titer greater than 217 and its subtype was IgG2b. The Western blotting and IFA results showed that the monoclonal antibody N2D5 only reacted with IBV, and were negative with Newcastle disease virus (NDV), infectious laryngotracheitis virus (ILTV), avian metapneumovirus (aMPV), infectious bursal disease virus (IBDV), avian leukosis virus (ALV) and Marek's disease virus (MDV). Monoclonal antibody N2D5 reacted with many genotypes in China and all 7 serotypes of IBV currently prevalent in Guangxi, including commonly used standard strains, vaccine strains and field strains. Immunohistochemistry showed that the virus signals could be detected in the trachea and kidney tissues of SPF chickens at different time after artificial infection of 3 representative IBV strains from chicken and 1 isolated strain from duck, which further proved its broad spectrum. [Conclusion] The monoclonal antibody N2D5 of IBV prepared based on hybridoma technology belongs to the IgG2b subtype. It has the characteristics of high specificity, wide response spectrum and strong binding ability with IBV. It can be used as a specific diagnostic antibody for clinical diagnosis of IBV and the study of virus distribution.
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In order to perform the isolation of avian infectious bronchitis virus (IBV) and study the pathogenicity of IBV isolate, the RT-PCR was used to detect nucleic acid extracted from a clinical sample of chickens, which were suspected to be infected with infectious bronchitis virus (IBV) and provided by a farmer in Yuncheng, Shanxi province. And the sample was detected as IBV positive by RT-PCR. Then 9-11-day-old SPF chicken embryonated eggs were inoculated with the sample filtered from the grinding fluid, and the obtained allantoic fluid was blindly passed by three generations (F3) and was also tested as IBV positive;The F11 generation passaged in embryonated eggs caused typical "dwarf embryo" lesions to SPF chicken embryonated eggs, and induced the loss of cilia in tracheal rings. The results showed that an IBV strain was isolated and named as YC181031. The S1 gene amplification and sequencing analysis showed that YC181031 strain belonged to IBV GI-22 genotype, which is also nephropathogenic type IBV. Seven-day-old SPF chicks were used to test the pathogenicity of the isolate. The results showed that several clinical symptoms were showed in chicks infected with YC181031, such as breathing with difficulty, depression, excreting watery droppings and death. The mortality of infected chicks was 20%. Typical pathological changes such as enlargement of kidney and urate deposition in the kidney were observed in infected chicks. The immunohistochemical assay and viral load detection were performed for the tissue samples from infected and dead chicks. The tissue lesions and distribution of virus were observed in the kidney, trachea, lung, glandular stomach, spleen and liver samples of infected chicks. RT-PCR detection of pharyngeal anal swabs showed that the virus shedding by infected chicks could be continuously detected within 14 days of the test period;The viral loads of various tissues were detected by RT-qPCR and the results showed that the viral load from high to low was kidney, trachea, lung, stomach, spleen and liver. The viral load of kidney was significantly higher than that of other tissues (P < 0.05).In this study, the pathogenicity characteristics of GI-22 genotype strain were systematically studied for the first time, providing a reference for the prevention and treatment of the disease.
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The most significant single nucleotide human leukocyte antigen genes polymorphisms and innate immunity genes associated with varying degrees of acute respiratory infection severity are considered-COVID-19 caused by the SARS-CoV-2 coronavirus. As data accumulated, it became clear that the SARS-CoV-2 virus exhibits significant regional, ethnic, and individual specificity. This is due to the population groups' genetic characteristics. This is necessary to reliably know the human genotype relationship with the COVID-19 course severity (asymptomatic, mild, moderate, severe, and extremely severe up to fatal outcomes) for more successful therapy and vaccination. At the same time, it was also known that the innate immunity system is on the first line of defense against the pathogenic penetration into the body, and the human leukocyte antigen system encodes molecules of the same name on the surface of cells that present various antigens, including viral infection pathogens, and determine the severity of the course of many diseases;therefore, these systems' genes. This approach makes it possible to assess the likelihood of a severe and extremely severe disease course in healthy and infected people, which in turn contributes to the correct therapy strategy, pharmacotherapy, and vaccination, as well as to create new antiviral therapeutic and preventive medicines. The genetically determined immune response heterogeneity to SARS-CoV-2 infection requires further study, since there is no unambiguous opinion about the leading mechanism that determines disease severity.
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The pandemic spread of African swine fever (ASF) has caused serious effects on the global pig industry. Virus genome sequencing and genomic epidemiology analysis play an important role in tracking the outbreaks of the disease and tracing the transmission of the virus. Here we obtained the full-length genome sequence of African swine fever virus (ASFV) in the first outbreak of ASF in China on August 3rd, 2018 and compared it with other published genotype II ASFV genomes including 9 genomes collected in China from September 2018 to October 2020. Phylogenetic analysis on genomic sequences revealed that genotype II ASFV has evolved into different genetic clusters with temporal and spatial correlation since being introduced into Europe and then Asia. There was a strong support for the monophyletic grouping of all the ASFV genome sequences from China and other Asian countries, which shared a common ancestor with those from the Central or Eastern Europe. An evolutionary rate of 1.312 × 10−5 nucleotide substitutions per site per year was estimated for genotype II ASFV genomes. Eight single nucleotide variations which located in MGF110-1L, MGF110-7L, MGF360-10L, MGF505-5R, MGF505-9R, K145R, NP419L, and I267L were identified as anchor mutations that defined genetic clusters of genotype II ASFV in Europe and Asia. This study expanded our knowledge of the molecular epidemiology of ASFV and provided valuable information for effective control of the disease.
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Objective: To understand the epidemiology and etiology of a cluster of cases with gastroenteritis in a nursing home in Anning district of Lanzhou, and to provide a scientific evidence for the prevention and control of norovirus diarrhea in community nursing centers. Methods: From January 28 to February 4 2021, an epidemiological investigation was conducted on all diarrhea cases, nursing staff and chefs in a nursing home in Anning district, Lanzhou city. Samples of patients' anal swabs, feces, vomitus were collected for norovirus detection by real-time fluorescent PCR. ORF1/ORF2 junction region of norovirus in some selected positive samples(Ct value 25) was sequenced. MEGA-X software was used to construct a phylogenetic tree for genetic evolution analysis using the neighboring method. Results: The first case was confirmed on January20,2021, and the number of cases peaked during January 25and 29.A total of 58 clinically diagnosed cases were reported,57were older people, with an incidence of(57/360,15.83%). Diarrhea(50/58,86.21%),vomiting(35/58,60.34%),nausea(13/58,22.41%)and abdominal pain(6/58,10.34%)were common symptoms, all cases were mild. Fifty-three asymptomatic cases were detected among chefs, housekeepers and nurses.A total of 163specimens were tested, the positive rate of norovirus GII was 49.08%(80/163). The positive rate of fecal samples collected from nurses, chefs and housekeepers was 48.62%(53/109), and was11.11%(2/18)in environmental surface swabs. The possibility of other pathogenic infections such as SARS-CoV-2was ruled out by further tests. Thirteen positive samples were selected for sequencing, and 9were successfully sequenced, they were all recombinant GII.4Sydney_2012 [P16]genotypes, forming an independent cluster, while in a large evolutionary branch with the 2020GII.10 [P16]and 2019GII.2 [P16]virus strains in Lanzhou city, showing a relative close genetic connection. Conclusions: GII .4Sydney_2012[P16]genotype of norovirus is found to be causative pathogen of this outbreak, and close contact is the main reason of the outbreak and persistence of the infection,so asymptomatic infections of norovirus play an important role in the disease spreading. Therefore, public health management in nursing homes and other centralized nursing facilities should be strengthened especially for asymptomatic workers in order to prevent virus transmission.
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Purple-fleshed sweet potato (PFSP) is a major staple food and feed material in tropical countries. The pandemic of COVID-19 that encouraged healthy lifestyles worldwide further increases the importance of PFSP. Despite its importance, the investment in research to improve PFSP in Indonesia was left behind. The objective of the research was to estimate the genetic variation and genetic distance of new PFSP genotypes prior to variety release. The research trials were arranged in a randomized block design, with nine new PFSP genotypes from polycrosses breeding as treatments and three check varieties in four growing environments in West Java, i.e., Cilembu, Jatinangor, Maja, and Karangpawitan during one season. Agronomic traits data were analyzed by the multivariate analysis. The principal component analysis (PCA) showed high genetic variation of PFSP in four environments. The eigenvalue ranges from 1.92 to 5.29 in Cilembu which contributed to 80.958% variability, 0.543–6.177 which contributed variability to 92.135% in Jatinangor, 0.824–5.695 in Karangpawitan which contributed to 92.117%, and 0.822–4.797 in Maja which contributed to 86.133%. Storage root length, storage root diameter, number of roots per plant, total root weight per plant, number of marketable/commercial roots, marketable/commercial root weight, number of roots per plot, and total storage root weight have a discriminant value of more than 0.7 in PC 1. Agglomerative hierarchical clustering (AHC) showed a wide distribution obtaining two clusters in Cilembu with euclidean distance 1.92–5.29, Jatinangor 1.72–6.09, Karangpawitan 1.28–6.38, and Maja 2.05–5.09. High genetic variation in the four environments greatly supports to the development of PFSP new varieties. [ FROM AUTHOR] Copyright of International Journal of Agronomy is the property of Hindawi Limited and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)
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AimHepatitis C Virus (HCV) infection is a major global health problem. Direct Acting Anti-viral therapy (DAA) has cure rates of 99% in adults and adolescents.1 DAAs were licensed for children 3 – 12 years during the recent coronavirus pandemic. In order to ensure equitable access and a safe, effective and convenient supply of these medications during lockdown, we established a virtual national treatment pathway for children with HCV in England and evaluated its feasibility, efficacy and treatment outcomes.MethodA paediatric Multidisciplinary Team Operational Delivery Network (pMDT ODN), supported by NHS England (NHSE), was established with relevant paediatric specialists, including pharmacists, to provide a single point of contact for referrals and information. Referral, treatment protocols and family friendly patient information were developed for all HCV therapy. On referral the pMDT ODN discussed and agreed the most appropriate DAA therapy based on clinical presentation and patient preferences, including ability to swallow tablets. Treatment was then prescribed and supplied in association with the local paediatrician and pharmacist, without the need for families to travel to national centres. All children were eligible for NHS funded therapy, each referring centre was approved by the pMDT ODN, prior to approval to dispense medication and funds were reclaimed via Blueteq authorisation. Demographic, clinical and social data was collected, and treatment outcomes were recorded. Feedback on feasibility and satisfaction on the pathway and supply of medication was sought from referrers.Results34 children were referred during the first six months;median (range) age 10 (3.9 – 14.5) years;15M;19F: Majority of referrals are HCV genotype type 1 (n=17) and 2 (n=12). DAA treatments prescribed: Sofosbuvir/Ledipasvir (n=21);Sofosbuvir/Velpatisvir (n=11) Glecaprevir/Pibrentasvir (n=2).27/34 confirmed as able to swallow tablets;3/7 have received training and are now able to successfully swallow tablets;4/7 are awaiting release of granules. All children who have completed treatment to date (11/27) have cleared virus at the end of treatment. Once the network was established, referrers found the virtual process easy to access. They valued being able to discuss their patients with the MDT providing a single point of contact with national specialists to discuss therapy. Specialist pharmacists within the pMDT were able to provide pharmaceutical information and support local Trusts to ensure safe, timely and funded supply of medication to children. There were three reported dispensing errors, where adult strength tablets were dispensed in error locally, however no doses were taken as parents noticed the error prior to giving a dose. A delay in availability of the granule or pellet formulations due to manufacturing delays during COVID, has meant a delay in referring and treating those children unable to swallow tablets.ConclusionPharmacists were a valuable resource within the National HCV Paediatric MDT Operational Delivery Network. They contributed expert knowledge on formulations and doses, supporting delivery of high-quality treatment and equity of access for children and young people with HCV in England. Education and awareness of new Paediatric formulations for local Pharmacy teams may prevent future dispensing errors.ReferenceNHS News 2021. Life saving hepatitis C treatment for children on the NHS. 24th August 2021. Available at: NHS England » Lifesaving hepatitis C treatment for children on the NHS [accessed 12th June 2022].
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AimRespiratory failure remains the most common cause of death in Cystic Fibrosis (CF) with chronic/complex infection a significant contributory factor. Infection frequency and associated treatment burden increase the risk drug-resistant organisms;however, stewardship strategies are challenging to translate to CF care.The CFTR modulator Kaftrio® (elexacaftor/tezacaftor/ivacaftor) launched in the UK in August 2020. Initial phase 3 clinical trials1 2 and a subsequent open-label extension study3 demonstrated promising data on health-related quality of life, including reduced pulmonary exacerbation (PEx) rates (63%), hospitalisation (71%) and PEx requiring IV antibiotics (78%). This evaluation aimed to provide a ‘real-world' review of the impact of Kaftrio® on IV antibiotic burden (admission rates, ‘bed-days', bed-day cost, total IV antibiotic use and ‘AWaRE' antibiotic use) in CF patients aged 12–16 years at a single tertiary centre.MethodA single-centre retrospective observational evaluation was conducted. All 12–16 year olds on Kaftrio® were identified using the local CF database. For each patient: month/year Kaftrio® commenced and prior CFTR modulator therapy were determined. Clinical trial patients were excluded. Digital clinical information systems were used to identify ‘chest-related' admissions for IV antibiotics in the 24 months prior to starting Kaftrio® and the treatment period post, up to June 2022. For each admission, drugs, doses administered and ‘IV antibiotic bed-days' were determined. ‘Bed-day' costs were calculated and use of ‘Restricted' or ‘Watch' antibiotics (WHO AWaRE/local Policy) were identified. IV antibiotic burden pre- and post Kaftrio® was evaluated.Results44 admissions in 33 patients were identified prior to Kaftrio®, compared with 13 admissions post-Kaftrio®, demonstrating a 65–70% overall reduction in admissions (PEx: rate 66/100patient/year vs 23/100patient/year). Pre-Kaftrio® 639 ‘bed days'/24 months were directly attributed to delivery of IV antibiotics-a total estimated cost of £383,400 (estimate £600/day/medical bed). From October 2020-June 2022, the number of IV antibiotic ‘bed days' fell to 183. A total reduction of 71%, with an estimated cost saving of £273,600. In the 24 months prior to Kaftrio® a total 2849 doses of IV antibiotics were administered vs 657 doses in the same patient cohort in the period post-Kaftrio® to June 2022, an absolute reduction of 2192 doses (77%). Of the 2849 IV antibiotics pre-Kaftrio® doses, 84% were restricted/watch antibiotics (R=706;W= 1681). Usage dropped by 37.5% and 89% respectively post-Kaftrio®.ConclusionResults suggest Kaftrio® reduces overall IV antibiotic burden in CF patients, providing real-word data supporting the phase 3 study outcomes. Significant reductions in PEx rates, IV antibiotic use, ‘bed days' and associated costs were all observed. Data demonstrated an absolute reduction in the use of ‘AWaRE' antibiotics, although use still accounts for a high overall proportion in this cohort. Results are limited by the data periods. Potential impact of the COVID-19 pandemic on PEx rates (‘shielding' population) should be considered. Nonetheless, the significance of these findings on overall outcomes and stewardship should not be downplayed. Ongoing review, including expanded patient populations (adults;6–11 years) is essential. Further works looking at oral antibiotics use, epidemiology, genotype and previous CFTR treatment would support extended evaluation of the overall impact of Kaftrio® on infection management in CF.ReferencesMiddleton PG, Mall MA, Drevineck P, et al. Elexacaftor-tezacaftor-ivacaftor for Cystic Fibrosis with a single Phe508del Allele. New England Journal of Medicine 2019;381:1809–1819.Southern K, Murphy J, Sinha I, et al. Corrector therapies (with or without potentiators) for people with cystic fibrosis with class II CFTR gene variants. Cochrane Database of Systematic Review 2020;12;1–313.Griese M, Costa, S, Linnemann R, et al. Safety and e ficacy of Elexacaftor/Tezacaftor/Ivacaftor for 24 weeks or longer in people with cystic fibrosis and one or more F598del Allele: Interim Results of an Open-Label Phase 3 Clinical Trial. American Journal of Respiratory and Critical Medicine 2021;203;381–384.
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Introduction: While complement is a contributor to disease severity in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, all three complement pathways might be activated by the virus. Lectin pathway activation occurs through different pattern recognition molecules, including mannan binding lectin (MBL), a protein shown to interact with SARS-CoV-2 proteins. However, the exact role of lectin pathway activation and its key pattern recognition molecule MBL in COVID-19 is still not fully understood. Methods: We therefore investigated activation of the lectin pathway in two independent cohorts of SARS-CoV-2 infected patients, while also analysing MBL protein levels and potential effects of the six major single nucleotide polymorphisms (SNPs) found in the MBL2 gene on COVID-19 severity and outcome. Results: We show that the lectin pathway is activated in acute COVID-19, indicated by the correlation between complement activation product levels of the MASP-1/C1-INH complex (p=0.0011) and C4d (p<0.0001) and COVID-19 severity. Despite this, genetic variations in MBL2 are not associated with susceptibility to SARS-CoV-2 infection or disease outcomes such as mortality and the development of Long COVID. Conclusion: In conclusion, activation of the MBL-LP only plays a minor role in COVID-19 pathogenesis, since no clinically meaningful, consistent associations with disease outcomes were noted.
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COVID-19 , Mannose-Binding Lectin , Humans , Post-Acute COVID-19 Syndrome , COVID-19/genetics , SARS-CoV-2 , Genotype , Lectins , Patient Acuity , Mannose-Binding Lectin/geneticsABSTRACT
Viruses remain the leading cause of acute gastroenteritis (AGE) worldwide. Recently, we reported the abundance of AGE viruses in raw sewage water (SW) during the COVID-19 pandemic, when viral AGE patients decreased dramatically in clinics. Since clinical samples were not reflecting the actual state, it remained important to determine the circulating strains in the SW for preparedness against impending outbreaks. Raw SW was collected from a sewage treatment plant in Japan from August 2018 to March 2022, concentrated by polyethylene-glycol-precipitation method, and investigated for major gastroenteritis viruses by RT-PCR. Genotypes and evolutionary relationships were evaluated through sequence-based analyses. Major AGE viruses like rotavirus A (RVA), norovirus (NoV) GI and GII, and astrovirus (AstV) increased sharply (10-20%) in SW during the COVID-19 pandemic, though some AGE viruses like sapovirus (SV), adenovirus (AdV), and enterovirus (EV) decreased slightly (3-10%). The prevalence remained top in the winter. Importantly, several strains, including G1 and G3 of RVA, GI.1 and GII.2 of NoV, GI.1 of SV, MLB1 of AstV, and F41 of AdV, either emerged or increased amid the pandemic, suggesting that the normal phenomenon of genotype changing remained active over this time. This study crucially presents the molecular characteristics of circulating AGE viruses, explaining the importance of SW investigation during the pandemic when a clinical investigation may not produce the complete scenario.
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COVID-19 , Enterovirus Infections , Enterovirus , Gastroenteritis , Norovirus , RNA Viruses , Rotavirus , Sapovirus , Viruses , Humans , Wastewater , Pandemics , Sewage , Viruses/genetics , Rotavirus/genetics , Norovirus/genetics , Sapovirus/genetics , Enterovirus Infections/epidemiology , Adenoviridae/genetics , Genotype , Phylogeny , FecesABSTRACT
Purpose: To investigate the epidemic variation of porcine epidemic diarrhea virus (PEDV) strains in Sichuan Province, and to analyze the causes of poor vaccination effect. Methods: Piglet intestinal samples were collected from a pig farm in Sichuan Province for PCR detection, virus purification, determination of virus titer and virus infection experiments. Whole genome sequencing of isolated strains was determined. The S gene sequence of the isolated strain was compared with the strains from other regions and vaccine strains, and the phylogenetic tree was established. The amino acid site variation of S protein between the isolated strain and the classical vaccine strain CV777 was compared. Results: A PEDV strain was successfully isolated and named as PEDV SNJ-P. The determination of virus titer was 1..107.5/100 L. Animal infection experiments showed that the isolated strain could cause diarrhea, dehydration and other symptoms and lead to death in piglets. Genome sequencing and phylogenetic tree analysis showed that the whole gene of PEDV SNJ-P strain was 28003 bp, and the genotype of the strain was S non-INDEL type. The strains were closely related to the strains of PEDV-WS, CH/JLDH/2016 and CH/HNLH/2015 isolated from China, and were relatively distant with the same type vaccine strain, and were far from the classical vaccine strain. Compared with the classical vaccine strain CV777, the S protein of SNJ-P strain had multiple amino acid mutations, deletions and insertions. Conclusion: Due to the continuous variation of strains, SNJ-P strain is far from the vaccine strain, and the current vaccines cannot provide effective protection. The results of this study are expected to provide reference for the study of PEDV strains and vaccine development in China.
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COVI D-19 has emerged as the most alarming infection of the present time instigated by the virus SARS-CoV-2. In spite of advanced research technologies, the exact pathophysiology and treatment of the condition still need to be explored. However, SARS-CoV-2 has several structural and functional similarities that resemble SARS-CoV and MERS-CoV which may be beneficial in exploring the possible treatment and diagnostic strategies for SARS-CoV-2. This review discusses the pathogen phenotype, genotype, replication, pathophysiology, elicited immune response and emerging variants of SARSCoV- 2 and their similarities with other similar viruses. SARS-CoV-2 infection is detected by a number of diagnostics techniques, their advantages and limitations are also discussed in detail. The review also focuses on nanotechnology-based easy and fast detection of SARS-CoV-2 infection. Various pathways which might play a vital role during SARS-CoV-2 infection have been elaborately discussed since immune response plays a major role during viral infections.
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Yield and yield attributes are important components in genotypic evaluation. The butterfly pea is a native plant of Indonesia, and it is considered an underutilized crop. The goals of this study were to evaluate genotypes using environment (year) interactions (GEIs) with yield and yield attributes, and evaluate butterfly pea genotypes based on stability measurements and sustainability index (SI). The study was conducted at the Ciparanje Experimental Field, Faculty of Agriculture, Universitas Padjadjaran using 35 butterfly pea genotypes in a randomized complete block design with two replications. The field trial was conducted over three years (2018–2020). The results showed that the yield and yield attributes were influenced by GEIs. Additive main effects and multiplicative interaction (AMMI) selected 11 stable genotypes (31.43%);genotype plus genotype by environment interaction (GGE) biplot, AMMI stability value (ASV), and genotype stability index (GSI), each selected six genotypes (17.14%) that were stable and high-yielding, and SI selected 18 genotypes (51.43%) that were stable and high-yielding. There were three genotypes identified by all measurements, namely G2, G14, and G16. These three genotypes can be selected as the superior genotypes of the butterfly pea for flower production, and can be used as material for crosses in plant-breeding prog.
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Introduction: Candida auris has been reported from various health care settings and has recently gained importance because of its intrinsic resistance to many classes of antifungal agents and to disinfection. The outbreak potential and high mortality associated with Candida auris infection reinforces the need for speciation. Routine conventional methods are cumbersome and automated systems are unable to confirm up to species level. Materials and Methods: Candida auris isolates from consecutive non-repetitive blood cultures over a 1-year period were speciated based on phenotypic, physiological and biochemical tests and VITEK. Molecular confirmation was done by PCR-RFLP and MALDI-TOF. Anti- fungal susceptibility test was performed according to CLSI guidelines (2021), using suitable controls. Virulence factors such as production of Hemolysin, Phospholipase, Esterase and Bio-film production were demonstrated. RT-PCR was used to screen the COVID-19 status using SD-Biosensor kit. Baseline data and clinical history were collected and analysed. Results: Of 3632 blood cultures (0.77%), 28 Candida sp. were isolated including 9 Candida auris, (9/28, 32.14%). Of these 8 were from COVID-19 positive patients (88.89%), while 1 was from COVID-19 negative patient (11.11%). Two patients survived, while the remaining 7 patients succumbed to the disease. Conclusion: The increasing incidence of Candidiasis especially during the COVID-19 pandemic has raised the concern for early speciation. Through multi-modal strategies such as quick and correct identification, active surveillance, guided reporting, stringent infection control measures and correct use of anti-fungals through proper susceptibility testing, we can prevent the occurrence and spread of new Candida auris cases in the future.
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The Indian poultry market is estimated to have an annual growth rate of 8.1% as of today. However, infectious diseases in poultry pose an important constraint in the growth and development of this sector in our region. Among infectious diseases, viral diseases of poultry pose a serious threat to the poultry industry from an economic point of view. Several viral disease outbreaks have been reported by various researchers from different parts of the country. Among the common viral diseases of poultry, incidences of Newcastle disease, Avian Influenza, Fowl Pox, Infectious Bursal Disease, Marek's disease, Infectious Bronchitis, Infectious Laryngotracheitis and Inclusion Body Hepatitis are significant in Assam as well as other parts of India. Thorough epidemiological studies followed by the identification of different serotypes, pathotypes, strains, etc. by genotyping and molecular characterization of viral disease pathogens may lead to ways to control and eradicate the diseases. Importance should be given to maintaining basic preventive measures like biosecurity, farm hygiene, and proper vaccination. In a developing country like India, disease outbreaks can impact the country's economy. In this study, a brief view of the common viral disease of poultry and its diagnosis and control strategies in Assam, India is depicted. However, this review well indicates a plethora of avian diseases that have occurred over the years causing a severe impact on poultry farming as a whole.
ABSTRACT
Coronavirus disease 2019 (COVID-19) continues to spread globally despite the discovery of vaccines. Many people die due to COVID-19 as a result of catastrophic consequences, such as acute respiratory distress syndrome, pulmonary embolism, and disseminated intravascular coagulation caused by a cytokine storm. Immunopathology and immunogenetic research may assist in diagnosing, predicting, and treating severe COVID-19 and the cytokine storm associated with COVID-19. This paper reviews the immunopathogenesis and immunogenetic variants that play a role in COVID-19. Although various immune-related genetic variants have been investigated in relation to severe COVID-19, the NOD-like receptor protein 3 (NLRP3) and interleukin 18 (IL-18) have not been assessed for their potential significance in the clinical outcome. Here, we a) summarize the current understanding of the immunogenetic etiology and pathophysiology of COVID-19 and the associated cytokine storm; and b) construct and analyze protein-protein interaction (PPI) networks (using enrichment and annotation analysis) based on the NLRP3 and IL18 variants and all genes, which were established in severe COVID-19. Our PPI network and enrichment analyses predict a) useful drug targets to prevent the onset of severe COVID-19, including key antiviral pathways such as Toll-Like-Receptor cascades, NOD-like receptor signaling, RIG-induction of interferon (IFN) α/ß, and interleukin (IL)-1, IL-6, IL-12, IL-18, and tumor necrosis factor signaling; and b) SARS-CoV-2 innate immune evasion and the participation of MYD88 and MAVS in the pathophysiology of severe COVID-19. The PPI network genetic variants may be used to predict more severe COVID-19 outcomes, thereby opening the door for targeted preventive treatments.
Subject(s)
COVID-19 , Antiviral Agents , Cytokine Release Syndrome , Humans , Immunogenetics , Interleukin-18 , NLR Family, Pyrin Domain-Containing 3 Protein , SARS-CoV-2ABSTRACT
The chronic infection hypothesis for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant emergence is increasingly gaining credence following the appearance of Omicron. Here, we investigate intrahost evolution and genetic diversity of lineage B.1.517 during a SARS-CoV-2 chronic infection lasting for 471 days (and still ongoing) with consistently recovered infectious virus and high viral genome copies. During the infection, we find an accelerated virus evolutionary rate translating to 35 nucleotide substitutions per year, approximately 2-fold higher than the global SARS-CoV-2 evolutionary rate. This intrahost evolution results in the emergence and persistence of at least three genetically distinct genotypes, suggesting the establishment of spatially structured viral populations continually reseeding different genotypes into the nasopharynx. Finally, we track the temporal dynamics of genetic diversity to identify advantageous mutations and highlight hallmark changes for chronic infection. Our findings demonstrate that untreated chronic infections accelerate SARS-CoV-2 evolution, providing an opportunity for the emergence of genetically divergent variants.