Single Virus Infection Research Articles

Epidemiological and etiological surveillance on infectious diarrhea in Pudong New Area, Shanghai, 2013-2017

Objective: To understand the epidemiological characteristics of infectious diarrhea pathogens in Pudong New Areas of Shanghai from 2013 to 2017 to provide evidence for control and prevention of the disease. Methods: From Jan 2013 to Dec 2017, active surveillance program on diarrhea was conducted in 14 sentinel hospitals (three tertiary-level and nine secondary-level, and two primary-level hospitals) in Pudong New Areas of Shanghai, based on location, catchment areas and number of patients. All recruited outpatients were interviewed in hospitals, using a standard questionnaire. Stool specimens were collected and tested for five viral and eight bacterial pathogens. Results: A total of 9 301 cases with infectious diarrhea were included, and the overall positive rate was 55.7% (5 179). Positive rates of single virus, single bacteria and mixed infections were 26.7% (2 481), 17.0% (1 579) and 12.0% (1 119), respectively. For single infection, the most commonly detected viruses appeared as norovirus (15.4%, 1 428/9 301) and rotavirus (7.2%, 667/9 301). The most commonly detected bacteria were diarrheagenic Escherichia coli (6.7%, 619/9 301) and non-typhoid Salmonella (3.3%, 305/9 301). The most common mixed infections were caused by virus-bacteria (4.9%, 459/9 301). Norovirus (17.0%, 838/4 938) showed the highest positive rates, followed by Escherichia coli (7.2%, 354/4 938), both seen in the age group of 20-59 years old group. Rotavirus (9.4%, 178/1 896) and non-typhoid Salmonella (4.9%, 93/1 896) were the most common pathogens found in the age group of 0-4 years old. The prevalence of norovirus peaked both in spring and autumn. The other peaks were seen as: Rotavirus in winter, diarrheagenic Escherichia coli in summer and non-typhoid Salmonella in summer. Conclusions: Our data showed that the positive rates of infectious diarrhea pathogens were high in Pudong New Areas of Shanghai from 2013 to 2017. The dominant pathogens would include norovirus, rotavirus and diarrheagenic Escherichia coli but with differenct distributions in age groups. Obvious seasonal patterns were also observed.

Metagenomic Analysis of Plant Viruses Associated With Papaya Ringspot Disease in Carica papaya L. in Kenya.

Carica papaya L. is an important fruit crop grown by small- and large-scale farmers in Kenya for local and export markets. However, its production is constrained by papaya ringspot disease (PRSD). The disease is believed to be caused by papaya ringspot virus (PRSV). Previous attempts to detect PRSV in papaya plants showing PRSD symptoms, using enzyme-linked immunosorbent assay (ELISA) and reverse transcriptase-polymerase chain reaction (RT-PCR) procedures with primers specific to PRSV, have not yielded conclusive results. Therefore, the nature of viruses responsible for PRSD was elucidated in papaya leaves collected from 22 counties through Illumina MiSeq next-generation sequencing (NGS) and validated by RT-PCR and Sanger sequencing. Viruses were detected in 38 out of the 48 leaf samples sequenced. Sequence analysis revealed the presence of four viruses: a Potyvirus named Moroccan watermelon mosaic virus (MWMV) and three viruses belonging to the genus Carlavirus. The Carlaviruses include cowpea mild mottle virus (CpMMV) and two putative Carlaviruses—closely related but distinct from cucumber vein-clearing virus (CuVCV) with amino acid and nucleotide sequence identities of 75.7–78.1 and 63.6–67.6%, respectively, in the coat protein genes. In reference to typical symptoms observed in the infected plants, the two putative Carlaviruses were named papaya mottle-associated virus (PaMV) and papaya mild mottle-associated virus (PaMMV). Surprisingly, and in contrast to previous studies conducted in other parts of world, PRSV was not detected. The majority of the viruses were detected as single viral infections, while a few were found to be infecting alongside another virus (for example, MWMV and PaMV). Furthermore, the NGS and RT-PCR analysis identified MWMV as being strongly associated with ringspot symptoms in infected papaya fruits. This study has provided the first complete genome sequences of these viruses isolated from papaya in Kenya, together with primers for their detection—thus proving to be an important step towards the design of long-term, sustainable disease management strategies.

Late viral or bacterial respiratory infections in lung transplanted patients: impact on respiratory function

BackgroundRespiratory infections are a major threat for lung recipients. We aimed to compare with a monocentric study the impact of late viral and bacterial respiratory infections on the graft function.MethodsPatients, who survived 6 months or more following lung transplantation that took place between 2009 and 2014, were classified into three groups: a viral infection group (VIG) (without any respiratory bacteria), a bacterial infection group (BIG) (with or without any respiratory viruses), and a control group (CG) (no documented infection). Chronic lung allograft dysfunction (CLAD) and acute rejection were analysed 6 months after the inclusion in the study.ResultsAmong 99 included lung recipients, 57 (58%) had at least one positive virological respiratory sample during the study period. Patients were classified as follows: 38 in the VIG, 25 in the BIG (among which 19 co-infections with a virus) and 36 in the CG. The BIG presented a higher initial deterioration in lung function (p = 0.05) than the VIG. But 6 months after the infection, only the VIG presented a median decrease of forced expiratory volume in 1 s; − 35 mL (IQR; − 340; + 80) in the VIG, + 140 mL (+ 60;+ 330) in the BIG and + 10 (− 84;+ 160) in the CG, p < 0.01. Acute rejection was more frequent in the VIG (n = 12 (32%)), than the BIG (n = 6 (24%)) and CG (n = 3 (8%)), p < 0.05, despite presenting no more CLAD (p = 0.21).ConclusionsDespite a less severe initial presentation, single viral respiratory infections seem to lead to a greater deterioration in lung function, and to more acute rejection, than bacterial infections.

Topological data analysis to model the shape of immune responses during co-infections

Co-infections by multiple pathogens have important implications in many aspects of health, epidemiology and evolution. However, how to disentangle the non-linear dynamics of the immune response when two infections take place at the same time is largely unexplored. Using data sets of the immune response during influenza-pneumococcal co-infection in mice, we employ here topological data analysis to simplify and visualise high dimensional data sets.We identified persistent shapes of the simplicial complexes of the data in the three infection scenarios: single viral infection, single bacterial infection, and co-infection. The immune response was found to be distinct for each of the infection scenarios and we uncovered that the immune response during the co-infection has three phases and two transition points. During the first phase, its dynamics is inherited from its response to the primary (viral) infection. The immune response has an early shift (few hours post co-infection) and then modulates its response to react against the secondary (bacterial) infection. Between 18 and 26 h post co-infection the nature of the immune response changes again and does no longer resembles either of the single infection scenarios.

The Role of Viral Coinfection in Bronchiolitis Treated With High-Flow Nasal Cannula at Pediatric Emergency Department During 2 Consecutive Seasons: An Observational Study.

The role of multiple respiratory viruses in bronchiolitis treated with high-flow nasal cannula (HFNC) has not been thoroughly investigated. We evaluated the contribution of coinfection on clinical course of bronchiolitis treated with HFNC and on response to this treatment. We selected 120 children with bronchiolitis, younger than 12 months, admitted to Emergency Department between 2016 and 2018 and treated with HFNC. We compared single and multiple virus infections in relation to specific outcomes such as the clinical response to HFNC and the HFNC failure. The multiple virus infection was defined by the detection of 2 or more viruses in nasopharyngeal aspirates. The HFNC failure was defined as escalation to higher level of care, including Helmet-Continuous Positive Airway Pressure, invasive ventilation or transfer to pediatric intensive care unit within 48 hours from the time of HFNC initiation. We also performed a comparison between HFNC failure and HFNC not-failure groups according to the number of virus and the type of virus. The severity score post-HFNC initiation was significantly associated with coinfection [odds ratio (OR): 1.361; 95% confidence interval (CI): 1.036-1.786; P = 0.027]. The likelihood of coinfection decreased by 23.1% for each increase of saturation O2 after HFNC initiation (OR: 0.769; 95% CI: 0.609-0.972; P = 0.028). Atelectasis was more likely to occur in coinfection (OR: 2.923; 95% CI: 1.049-8.148; P = 0.04). The duration of HFNC treatment increased significantly in coinfection (OR: 1.018; 95% CI: 1.006-1.029; P = 0.002). No significant differences were described between HFNC failure and the number and the type of detected viruses. The detection of multiple viruses and the type of virus did not influence the HFNC failure, although the coinfection was associated with a deterioration of severity score, a longer HFNC treatment and a major presence of atelectasis. The role of coinfection on HFNC treatment might subtend a complex interplay between multiple viruses and host susceptibility.

Association between multiple respiratory viral infections and pediatric intensive care unit admission among infants with bronchiolitis

BackgroundIt is unclear whether multiple respiratory viral infections are associated with more severe bronchiolitis requiring pediatric intensive care unit (PICU) admission. We aimed to identify the association between multiple respiratory viral infections and PICU admission among infants with bronchiolitis. MethodsWe performed a 1:1 case-control study enrolling previously healthy full-term infants (≤12 months) with bronchiolitis admitted to the PICU as cases and those to the general pediatric ward as controls from 2015 to 2017. Multiplex polymerase chain reaction (PCR) was used for detection of the respiratory viruses. We summarized the characteristics of infants admitted to the PICU and the general pediatric unit. Multivariable logistic regression analysis was used to fit the association between multiple respiratory viral infections (≥2 strains) and PICU admission. ResultsA total of 135 infants admitted to the PICU were compared with 135 randomly selected control infants admitted to the general pediatric unit. The PICU patients were younger (median: 2.2 months, interquartile range: 1.3–4.2) than the general ward patients (median: 3.2 months, interquartile range: 1.6–6.4). Respiratory syncytial virus (74.1%), rhinovirus (28.9%), and coronavirus (5.9%) were the most common viruses for bronchiolitis requiring PICU admission. Patients with bronchiolitis admitted to the PICU tended to have multiple viral infections compared with patients on the general ward (23.0% vs. 10.4%, P<0.001). In the multivariable logistic regression analysis, bronchiolitis with multiple viral infections was associated with higher odds of PICU admission (adjusted odds ratio: 2.56, 95% confidence interval: 1.17–5.57, P=0.02). ConclusionInfants with multiviral bronchiolitis have higher odds of PICU admission compared with those with a single or nondetectable viral infection.

Comparison of Rates of Hospitalization Between Single and Dual Virus Detection in a Mexican Cohort of Children and Adults With Influenza-Like Illness.

BackgroundMolecular detection methods allow for the simultaneous detection of several infectious agents. This study assesses whether co-infection with 2 viruses as compared with 1 is associated with increased hospitalization in those with acute respiratory infections.MethodsWe prospectively enrolled a cohort of pediatric and adult participants with influenza-like illness during 2010–2014 in Mexico. Clinical information and respiratory samples were collected at enrollment. Respiratory viruses were detected with multiplex polymerase chain reaction (PCR) and influenza-specific reverse transcription PCR assays. Participants were followed for 14 and 28 days after inclusion. Severity of disease, as measured by hospitalization with acute respiratory infections, was compared between single and dual viral infections.ResultsAmong 5662 participants in the study, either 1 (n = 3285) or 2 (n = 641) viruses were detected in 3926 participants. Rhinovirus (n = 1433), influenza (n = 888), and coronaviruses (n = 703) were the most frequently detected viruses (either alone or in co-infection). Bocavirus, respiratory syncytial virus (RSV), metapneumovirus, and rhinovirus cases were hospitalized more often than other viruses. Bocavirus+rhinovirus cases were hospitalized more often than those with rhinovirus alone (but not bocavirus alone). RSV cases were more likely to be hospitalized than cases with co-infections of RSV and parainfluenza virus or coronavirus. Metapneumovirus cases were hospitalized more often than those co-infected with metapneumovirus+coronavirus.ConclusionsIn this study, detection of 2 viruses did not significantly increase hospitalizations compared with single virus infections. Larger studies will allow for distinguishing between sequential and simultaneous infection and for a better understanding of the role of each virus during the evolution of acute respiratory episodes.

Germination and Longevity of Some Cowpea Cultivars Affected by Single and Mixed Virus Infections in Niger State, Nigeria

Cowpea being a dependable source of protein for human growth and development is widely cultivated in sub-Saharan Africa including Nigeria. In spite of its numerous uses, infection by viruses constitutes serious problems to its productivity and once plants are infected, there is no remedy as is with other pathogens such as bacteria, fungi and nematodes. A field trial was conducted to investigate the reactions of twenty five cowpea cultivars to single and mixed infections with two unrelated viruses: Blackeye cowpea mosaic virus (BlCMV) and Cowpea mottle virus (CPMoV) on seed germination and longevity. The trial was conducted at the Teaching and Research Farm of the Ahmadu Bello University (ABU), Zaria, Mokwa Station and set up in a randomized complete block design (RCBD) with three replicates. For the single virus infection, seedlings of the twenty five cultivars were inoculated at 10 days after sowing (DAS), while for the mixed virus infections, seedlings were inoculated at 10 and 17 DAS. Results showed that all the cultivars were susceptible to single and mixed infections but to seemingly different extents. Germination of seeds was generally high before storage but was short lived indicating that conservation of infected seeds of the cultivars was impaired. Seeds of cultivars IT04K-267-8 and IT07K-222-2 recorded germination percentages of 54.6 and 53.7% respectively, while cultivars IT96D-610 and IT04K-291-2 had germination values of 52% which did not differ from each other. Viability of seeds amongst the 25 test cowpea cultivars from single infection with CPMoV alone and BICMV alone did not differ in some instances. Percent germination in cultivars IT98K-205-M8, IT90K-277-2 and IT07K-222-2 inoculated with BICMV + CPMoV were not much affected. Test of accelerated ageing germination (AAG) percentage for four weeks showed that seed vigour was greatly impaired in cultivars IT07K-292-2-10, IT06K-124 and IT90K-277-2 infected with BICMV + CPMoV compared to the lowest AAG percentage of 31.6 recorded in seeds of cultivar IT99K-377-1. Constant monitoring of legume fields through regular field sanitation and disease surveys to identify new and emerging viruses as facts obtained from this study are good starting point for legume virus diseases diagnosis.

New approach of electrotherapy for grapevine virus elimination

Electrotherapy in a horizontal electrophoresis tank was applied to remove single and mixed virus infections in grapevine cultivars (Vitis vinifera L.). Electric stimulation of grapevine herbaceous cuttings with electric current of 40-100 mA, for 5-20 min treatment time was followed by in vitro regeneration of new plants. ELISA negative grapevines were obtained in different percentages, depending on the virus infection type and experimental parameters. While the Grapevine fleck virus was removed up to 100%, Grapevine fanleaf virus-free plants were obtained between 44 and 50%, and the lowest virus elimination rate of 25-30% was registered for Grapevine leafroll associated virus type 1. The complex consisting of Grapevine fleck virus and Grapevine virus A was eliminated in 50% of recovered plants.

Identification of an H1N1 subtype of swine influenza virus and serological analysis

To investigate the epizootic of swine influenza virus (SIV), 60 nasal swabs were collected from a clinical cases of pig farm in Tai'an City, Shandong Province of China in April 2017. SIV was isolated by inoculating into 10-day-old Special Pathogen Free embryonated eggs and the whole genome was sequenced. An H1N1 subtype SIV was isolated and designated as A/swine/Shandong/TA04/2017(H1N1). Phylogenetic analysis showed that apart from the polymerase A (PA) fragment belonging to the 2009 pandemic H1N1 branch, seven genome segments belonged to avian-like H1N1 influenza virus lineage. The cleavage site sequence of the hemagglutinin (HA) protein was PSIQSR↓G, which is a typical molecular biological characteristic. Five potential N-glycosylation sites (N14, N26, N277, N484 and N543) were found in the HA gene. To further investigate the epidemiology of SIV in this farm, the 995 serum samples were assessed with EAH1N1 2009 pandemic H1N1 and H3N2 antigens. The results showed that the total positive rate was 65.43%. The positive rates of single virus infection detected by EAH1N1, 2009pdmH1N1 and H3N2 for serum HI (Hemagglutination inhibition) were 48.35, 30.85 and 7.47%, respectively. The results showed that SIV in Shandong Province has been reassorted in some segments and the SIV-positive rate was high on the SIV outbreak farm. These data provide evidence of an epizootic of SIV.

Co-infections, genetic, and antigenic relatedness of avian influenza H5N8 and H5N1 viruses in domestic and wild birds in Egypt

ABSTRACTA total of 50 poultry farms of commercial broilers (N = 39) and commercial layers (N = 11) suffered from respiratory problems and mortality during the period from January 2016 to December 2017 were investigated. Also, samples were collected from quail (N = 4), Bluebird (Sialis, N = 1), and Greenfinch (Chloris chloris, N = 1) for analysis. Respiratory viral pathogens were screened by PCR and positive samples were subjected to virus isolation and genetic identification. Antigenic relatedness of isolated avian influenza (AI) H5 subtype was evaluated using cross-hemagglutination inhibition. Results revealed that the incidence of single virus infections in commercial broilers was 64.1% (25/39), with the highest incidence for ND (33.3%) and H9N2 (20.5%), followed by H5N1 (7.7%) and H5N8 (2.7). Meanwhile, H9N2/ND mixed infection was the most observed case (7.7%). Other mixed infections H5N1/ND, H5N1/H9N2/ND, H5N1/H9N2/ND/IB, H9N2/IB, and H9N2/ILT were also observed (2.6% each). In commercial layers, H5N1 and ILT were the only detected single infections (18.1% each). Mixed H9N2/ND was the most predominant infection in layers (27.3%). Other mixed infections of H9N2/IB, H5N1/H5N8/H9N2, and H9N2/ND/IB were observed in 3 separate farms (9.1% each). The H5N8 virus was detected in one quail farm and 2 out of 3 wild bird's samples. Partial HA gene sequence analysis showed the clustering of the selected AI H5N8 within the 2.3.4.4 clade, while H5N1 clustered with the clade 2.2.1.2. Interestingly, the H5N8 isolated from chickens possessed 6 amino acids substitutions at HA1 compared to those isolated from wild birds with low antigenic relatedness to AI H5N1 clades 2.2.1 or 2.2.1.2. In conclusion, mixed viral infections were observed in both broiler and layer chickens in Egypt. The detected triple H5N1, H9N2, and H5N8 influenza co-infection raises the concern of potential AI epidemic strain emergence. The low genetic and antigenic relatedness between AI H5N1 and H5N8 viruses suggest the need for modification of vaccination strategies of avian influenza in Egypt along with strict biosecurity measures.

Seasonal dynamics and spatial distribution of main Grapevine viruses in field-grown grapevine cultivars

Propagation of uninfected plant material is one of the most effective ways for controlling grapevine disease. Different diagnostic methods are available for testing viral infections, including serological techniques such as enzyme-linked immunosorbent assay (ELISA) and molecular techniques based on reverse transcription polymerase chain reaction (RT-PCR) and reverse transcription quantitative PCR (RT-qPCR). The objective of this study was to examine seasonal dynamics and spatial distribution of grapevine viruses within field-grown grapevine cultivars, in order to make more efficient virus detection by ELISA and RT-PCR, by identifying and selecting proper plant material and sampling time. For this purpose, a systematic investigation, considering different plant tissues and phenological stages, has been carried out through a multi-year study. Eight grapevine plants with single or multiple viral infections were selected and their state of infection was firstly monitored during the 2007 growing season, followed by a final infection assessment occurred after 5 years. Our results confirmed a strong erratic distribution of viruses within the vines, regardless of sampling stages, tissue type and/or different plant parts. For what concerns seasonal dynamics, our results on long-term infected grapevine plants corroborated the hypothesis that viruses behave differently from each other with respect to their irregular or rather homogeneous spatial distribution. Thus, an accurate sanitary status check of any grapevine must provide several random samples from different plant parts that have to be carried out several times both during a single growing season and through the years, removing infected vines, and taking vector populations under control.

Effect of stochasticity on coinfection dynamics of respiratory viruses

BackgroundRespiratory viral infections are a leading cause of mortality worldwide. As many as 40% of patients hospitalized with influenza-like illness are reported to be infected with more than one type of virus. However, it is not clear whether these infections are more severe than single viral infections. Mathematical models can be used to help us understand the dynamics of respiratory viral coinfections and their impact on the severity of the illness. Most models of viral infections use ordinary differential equations (ODE) that reproduce the average behavior of the infection, however, they might be inaccurate in predicting certain events because of the stochastic nature of viral replication cycle. Stochastic simulations of single virus infections have shown that there is an extinction probability that depends on the size of the initial viral inoculum and parameters that describe virus-cell interactions. Thus the coinfection dynamics predicted by the ODE might be difficult to observe in reality.ResultsIn this work, a continuous-time Markov chain (CTMC) model is formulated to investigate probabilistic outcomes of coinfections. This CTMC model is based on our previous coinfection model, expressed in terms of a system of ordinary differential equations. Using the Gillespie method for stochastic simulation, we examine whether stochastic effects early in the infection can alter which virus dominates the infection.ConclusionsWe derive extinction probabilities for each virus individually as well as for the infection as a whole. We find that unlike the prediction of the ODE model, for similar initial growth rates stochasticity allows for a slower growing virus to out-compete a faster growing virus.

A multiplex RT-PCR assay for rapid and simultaneous detection of four RNA viruses in swine

A multiplex reverse transcription polymerase chain rection (mRT-PCR) was developed for simultaneous detection of four RNA viruses in swine. The conserved target sequences directed to classical swine fever virus (CSFV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea virus (PEDV) and transmissible gastroenteritis coronavirus (TGEV) were selected based on alignments of genomic sequences and then specific primers were designed. The mRT-PCR assay was developed and evaluated for its specificity and sensitivity. The expected product from the single viral template was amplified by mRT-PCR and no spurious PCR amplification occurred from the genomic RNA or DNA of other pathogens. For single virus or different combinations of two viruses the detection limit of mRT-PCR was consistent with a single RT-PCR wtith 1 × 103 copies. For different combinations of the three viruses or four viruses, sensitivity of PEDV detection partially decreased. All of positive clinical specimens by the mRT-PCR were identically confirmed using Taqman RT-qPCR. Therefore, the mRT-PCR is a useful tool for epidemiological studies and laboratory diagnosis of single virus and/or mixed infections in swine.

Occurrence and Molecular Variability of Kiwifruit Viruses in Actinidia deliciosa 'Xuxiang' in the Shaanxi Province of China.

Kiwifruit (Actinidia spp.) is an economically substantial fruit crop with China the main producer. China is the primary source of wild kiwifruit and the largest producer of kiwifruit in terms of both production and planting area, and Shaanxi province is the largest kiwifruit producer in China. Previous studies reported presence of kiwifruit viruses in Actinidia chinensis. In this study, six viruses were identified in kiwifruit 'Xuxiang' (A. deliciosa) in Shaanxi, China. The incidence, distribution, and genetic diversity of these viruses were studied. The results showed that Actinidia virus A (AcVA), Actinidia virus B (AcVB), Actinidia chlorotic ringspot-associated virus (AcCRaV), cucumber mosaic virus (CMV), apple stem grooving virus (ASGV), and potato virus X (PVX) were the main viruses infecting Xuxiang kiwifruit in Shaanxi, China. Incidence of the various viruses with both single and multiple infection varied with different kiwifruit-growing counties. For single virus infection, the highest and the lowest numbers of samples infected were about 22 for AcCRaV and 0 for AcVB in Meixian out of 170 samples, 12 for AcVA and 0 for CMV in Zhouzhi out of 120 samples, 10 for AcVA and 0 for AcVB, AcCRaV, ASGV, PVX, and CMV in Yangling out of 70 samples, and 8 for AcCRaV and CMV and 0 for AcVA, AcVB, ASGV, and PVX in Hanzhong out of 80 samples, respectively. Samples which were multiply infected with two or more viruses were also detected. Analysis of the phylogenetic tree of these viruses showed some genetic variability in the AcVA, AcVB, and AcCRaV isolates of Shaanxi kiwifruit. There was no obvious molecular variation in the coat protein genes of ASGV, CMV, and PVX virus isolates from Shaanxi kiwifruit. The present study is the first large-scale survey of kiwifruit viruses in Shaanxi, China. To our knowledge, this is the first report of PVX infecting kiwifruit and the first report of molecular variability of AcVA, AcVB, and AcCRaV. These results provide important data for studying the genetic evolution of AcVA, AcVB, AcCRaV, ASGV, CMV, and PVX.

Diversity of respiratory viruses detected among hospitalized children with acute lower respiratory tract infections at Hospital Serdang, Malaysia

BackgroundThe role of respiratory viruses as the major cause of acute lower respiratory tract infections (ALRTIs) in children is becoming increasingly evident due to the use of sensitive molecular detection methods. The aim of this study was to use conventional and molecular detection methods to assess the epidemiology of respiratory viral infections in children less than five years of age that were hospitalized with ALRTIs. MethodsThe cross-sectional study was designed to investigate the occurrence of respiratory viruses including respiratory syncytisl virus (RSV), human metapneumovirus (HMPV), influenza virus A and B (IFV-A and B), parainfluenzavirus 1, 2, 3 and 4 (PIV 1, 2, 3 and 4), human rhinoviruses (HRV), human enterovirus (HEV), human coronaviruses (HCoV) 229E and OC43, human bocavirus (HBoV) and human adenovirus (HAdV) in hospitalized children with ALRTIs, at Hospital Serdang, Malaysia, from June 16 to December 21, 2009. The study was also designed in part to assess the performance of the conventional methods against molecular methods. ResultsViral pathogens were detected in 158 (95.8%) of the patients. Single virus infections were detected in 114 (67.9%) patients; 46 (27.9%) were co-infected with different viruses including double-virus infections in 37 (22.4%) and triple-virus infections in 9 (5.5%) cases. Approximately 70% of samples were found to be positive using conventional methods compared with 96% using molecular methods. A wide range of respiratory viruses were detected in the study. There was a high prevalence of RSV (50.3%) infections, particularly group B viruses. Other etiological agents including HAdV, HMPV, IFV-A, PIV 1–3, HBoV, HCoV-OC43 and HEV were detected in 14.5, 9.6, 9.1, 4.8, 3.6, 2.4 and 1.8 percent of the samples, respectively. ConclusionOur results demonstrated the increased sensitivity of molecular detection methods compared with conventional methods for the diagnosis of ARTIs in hospitalized children. This is the first report of HMPV infections in Malaysia.

Sequencing and assembly of small RNAs reveal the presence of several begomoviruses, potyviruses, badnaviruses and mastreviruses in the sweet potato leaf virome in Barbados

Sweet potato [Ipomoea batatas (L.) Lam] is increasingly becoming an important food and industrial crop worldwide that is affected by over thirty viruses belonging to different virus families. Little is known about these viruses on the many local and commercial sweet potato cultivars in the Caribbean, including Barbados. Therefore, polymerase chain reaction (PCR) and small RNA sequencing and assembly (sRSA) were used to detect viruses in the sweet potato leaf virome in Barbados. The viruses detected by sRSA were mainly from two virus families in sweet potato: Geminiviridae (genus Begomovirus) and Caulimoviridae (genus Badnavirus). Together, these viruses accounted for more than 75% of the virus contigs found in the sweet potato leaf virome in Barbados. Although sweet potato feathery mottle virus (SPFMV, genus Potyvirus, family Potyviridae) was frequently detected by PCR in infected leaf samples, only 10% of the sequenced contigs matched to these viruses in the leaf virome. The results suggest the absence of the sweet potato virus disease complex (SPVD) in Barbados but reveal possibly new, severe single virus infections or emerging virus associations in the virome largely composed of begomoviruses, badnaviruses, potyviruses and mastreviruses previously unreported in sweet potato in the Caribbean.

Is multiple viral infection a predictor of severity in children with acute bronchiolitis?

Background:Acute bronchiolitis is a common cause of pediatric emergency department admissions in children younger than 2.Objectives:The study aimed to compare the outcomes and the severity of bronchiolitis in young children with multiple simultaneous respiratory virus infections to those with single virus infection and no virus identified group.Methods:Patients with moderate and severe bronchiolitis who visited our emergency department between November 2016 and May 2017 had nasopharyngeal swab samples results tested by multiplex polymerase chain reaction were included in the study. Patients’ characteristics, clinical severity of illness, and outcome (pediatric emergency department discharge, admission to ward or pediatric intensive care unit) were compared with the detected viral agents.Results:A total of 241 patients were included in the study. The mean age was 7.8 ± 2.6 months and 147 (61%) were male. Respiratory syncytial virus was the most common detected viral agent in 108 (39%) cases followed by human rhinoviruses in 67 (24%). Respiratory syncytial virus was found more frequently in February and March (p = 0.002). Leukocytosis and pneumonia were more likely observed in patients with only human rhinoviruses (+) subjects (p = 0.010 and p = 0.015, respectively). Intensive care hospitalization rate (16%) was higher in patients with multiple viral agents (p = 0.004).Conclusions:Respiratory syncytial virus remains the most common detected viral agent in acute bronchiolitis patients. While the pathogens detected were seasonally different, there was a significant relationship between leukocytosis, bacterial pneumonia, and detected viral agents. The disease was more severe in patients with multiple viral agents.

Yield evaluation of multiple and co-infections of begomoviruses and potyviruses on sweet potato varieties under field conditions and confirmation of multiple infection by NGS

Potyviruses and begomoviruses are regarded as the most common viruses affecting sweet potato production in South Africa (SA). The impact of single and mixed virus infections on the yield of sweet potato varieties have not been established in SA. The objective of this study was to determine the effects of potyviruses and begomoviruses on sweet potato total and marketable yield. Twelve varieties, 8 locally bred and four imported, were selected for evaluations and these were graft-infected with different virus combinations: 1) co-infections of the russet crack (RC) strain of Sweet potato feathery mottle virus (SPFMV) + Sweet potato virus G (SPVG) + Sweet potato virus C (SPVC) + begomoviruses [Sweet potato leaf curl Sao Paulo virus (SPLCSPV) + Sweet potato mosaic virus (SPMV)] [(treatment (T) 1)]; 2) co-infections of SPFMV (RC strain) + begomoviruses (T2); 3) single infection of the RC strain of SPFMV (T3); and 4) co-infection of the begomoviruses SPLCSPV and SPMV (T4). Next generation sequencing (NGS), reverse transcription polymerase chain reaction (RT-PCR) or PCR confirmed the identification of the viruses in sweet potato plants used as sources of various treatments. Two consecutive field trials were planted in January 2014 and 2015, respectively. Varieties produced significantly reduced total [(F11, 236 = 5.17); P < 0.0001)] and marketable [(F11, 236 = 3.65); P < 0.0001)] yield with all the treatments in both the trials. Treatment 1 reduced the total yield by between 66% and 93% in trial 1, and by 66% and 99.5% in trial 2. The loss in marketable yield ranged between 67% and 98% in trial 1, and 58% and 100% in trial 2 with T1. Treatment 2 also led to reduced average total yield of varieties by between 28% and 94% in trial 1 and the total yield was severely reduced by between 74% and 99% in trial 2. Similar trends were recorded for the marketable yield of varieties treated with T2. The total yield reduced with T3 was between 27% and 78% in trial 1 and varieties such as Bophelo, Hernandez, Impilo and Ribbok had yield reduction of less than 50% when compared to the other eight varieties, however, total yield was severly reduced in trial 2 (61%–99%) for all varieties. Similar trends were also observed with marketable yield of varieties treated with T3. Total yield was also reduced with begomovirus co-infections (T4) and yield loss was between 32% and 84% in trial 1 and varieties such as Bophelo, Bosbok, Mvuvhelo, Ndou and Resisto had yield reduction of less than 50% when compared to the other seven varieties. Total yield was severely reduced in trial 2 with T4 and only varieties 199062.1 and Hernandez had yield reduction of less than 50%. Marketable yield was also reduced with T4 and only varieties Bophelo, Bosbok, Mvuvhelo and Ndou had yield reduction of less than 50% in trial 1. The results demonstrate that single or co-infections of potyviruses and begomoviruses have variable negative effects on the yield of sweet potato varieties.

Resistance of advanced cassava breeding clones to infection by major viruses in Uganda

Cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) are two viral diseases that cause severe yield losses in cassava of up to 100%, thereby persistently threatening food and income security in sub-Saharan Africa. For effective management of these diseases, there is a critical need to develop and deploy varieties with dual resistance to CBSD and CMD. In this study, we determined the response of advanced breeding lines to field infection by cassava brown streak viruses (CBSVs) and cassava mosaic begomoviruses (CMBs). This aim helped in identifying superior clones for downstream breeding. In total, 220 cassava clones, three in uniform yield trials (UYTs) and 217 in a crossing block trial (CBT), were evaluated for virus and disease resistance. Field data were collected on disease incidence and severity. To detect and quantify CBSVs, 448 and 128 leaf samples from CBSD symptomatic and symptomless plants were analyzed by reverse transcription PCR and real-time quantitative PCR, respectively. In addition, 93 leaf samples from CMD symptomatic plants in the CBT were analyzed by conventional PCR using CMB species-specific primers. In the CBT, 124 (57%) cassava clones did not express CMD symptoms. Of the affected plants, 44 (55%) had single African cassava mosaic virus infection. Single Cassava brown streak virus (CBSV) infections were more prevalent (81.6%) in CBT clones than single Ugandan cassava brown streak virus (UCBSV) infection (3.2%). Of the three advanced clones in the UYT, NAROCASS 1 and NAROCASS 2 had significantly lower (P < 0.05) CBSD severity, incidence, and CBSV load than MH04/0300. In the UYT, only 22% of samples tested had CBSVs, and all showed a negative result for CMBs. The low disease incidence, severity, and viral load associated with NAROCASS 1 and NAROCASS 2 is evidence of their tolerance to both CBSD and CMD. Therefore, these two cassava clones should be utilized in CBSD and CMD management in Uganda, including their utilization as progenitors in further virus resistance breeding.