Incidence Of Virus Research Articles

Impact of climate change on West Nile virus distribution in South America.

West Nile virus (WNV) is a vector-borne pathogen of global relevance and is currently the most widely distributed flavivirus causing encephalitis worldwide. Climate conditions have direct and indirect impacts on vector abundance and virus dynamics within the mosquito. The significance of environmental variables as drivers in WNV epidemiology is increasing under the current climate change scenario. In this study we used a machine learning algorithm to model WNV distributions in South America. Our model evaluated eight environmental variables for their contribution to the occurrence of WNV since its introduction in South America in 2004. Our results showed that environmental variables can directly alter the occurrence of WNV, with lower precipitation and higher temperatures associated with increased virus incidence. High-risk areas may be modified in the coming years, becoming more evident with high greenhouse gas emission levels. Countries such as Bolivia, Paraguay and several Brazilian areas, mainly in the northeast and midwest regions and the Pantanal biome, will be greatly affected, drastically changing the current WNV distribution. Understanding the linkages between climatological and ecological change as determinants of disease emergence and redistribution will help optimize preventive strategies. Increased virus surveillance, integrated modelling and the use of geographically based data systems will provide more anticipatory measures by the scientific community.

Simulation model for the dynamics of dengue with asymptomatic transmission and the effect of temperature

Background: One of the fastest spreading vector-borne diseases in tropical and subtropical regions is dengue, which generates cost overruns for public health entities. Several factors can influence the dynamics of dengue virus transmission: environmental and climatic (abundance of vectors), interactions between hosts (infections by asymptomatic individuals), and population immunological factors. Given these conditions, it is necessary to carry out theoretical studies based on meteorological factors and asymptomatic transmission that are associated with both the existence of the vector and its incidence, in order to provide a scientific basis for health entities in decision-making. Methods: A mathematical model based on nonlinear ordinary differential equations is proposed to interpret the dynamics of dengue transmission in humans coupled to the dynamics of the Aedes aegypti species, considering the population of symptomatic and asymptomatic infected humans and the effect of temperature variability. The basic reproduction number was found and some simulation results based on the Runge-Kutta numerical method were obtained. Results: The simulations showed that the temperature had a directly proportional relationship with the basic reproduction number. The cases of infected people and carrier mosquitoes increased when the temperature peaks increased drastically; in low temperatures the infection persisted with low morbidity due to the survival of asymptomatic people. Conclusions: High temperatures tolerable by mosquitoes increase their life expectancy and their numbers in the environment which, together with a reservoir of asymptomatic infected people, leads to a higher incidence of the dengue virus in certain seasons or maintains its circulation in seasons of low temperatures, despite lower vector survival rates.

Distance to public transit predicts spatial distribution of dengue virus incidence in Medellín, Colombia

Dengue is a growing global threat in some of the world’s most rapidly growing landscapes. Research shows that urbanization and human movement affect the spatial dynamics and magnitude of dengue outbreaks; however, precise effects of urban growth on dengue are not well understood because of a lack of sufficiently fine-scaled data. We analyzed nine years of address-level dengue case data in Medellin, Colombia during a period of public transit expansion. We correlate changes in the spread and magnitude of localized outbreaks to changes in accessibility and usage of public transit. Locations closer to and with a greater utilization of public transit had greater dengue incidence. This relationship was modulated by socioeconomic status; lower socioeconomic status locations experienced stronger effects of public transit accessibility and usage on dengue incidence. Public transit is a vital urban resource, particularly among low socioeconomic populations. These results highlight the importance of public health services concurrent with urban growth.

Changes in Critical Bronchiolitis After COVID-19 Lockdown.

IntroductionIn response to the coronavirus disease 2019 (COVID-19) pandemic, state and local governments implemented mitigation strategies, including lockdowns, thereby averting the typical fall/winter 2020 bronchiolitis season and reducing the incidence of respiratory viruses, such as respiratory syncytial virus (RSV). Florida implemented a strict lockdown from April 1, 2020, to April 30, 2020. The removal of lockdown precautions on September 25, 2020, was followed by an atypical out-of-season surge of bronchiolitis in April 2021. Anecdotally, this surge appeared to be associated with both increased poly-viral coinfections and disease severity.ObjectiveTo determine if the bronchiolitis out-of-season surge differed from historical seasonal case patterns.MethodsA single-center retrospective cohort study of admissions to the pediatric intensive care unit (PICU) with International Classification of Diseases, Tenth Revision (ICD-10) codes of bronchiolitis, from December 9, 2019, to February 29, 2020 (12 weeks, pre-lockdown group or PreLD), was compared to March 29, 2021, to June 19, 2021 (12 weeks, post-lockdown group or PostLD). Variables used for comparison were gender, ethnicity, age, viral coinfections, viruses detected, PICU length of stay, hospital length of stay, mortality, maximum respiratory support needed, mechanical ventilation days, extracorporeal life support (ECLS) days, and severity of disease measured by Pediatric Logistic Organ Dysfunction-2 (PELOD-2) and Pediatric Sequential Organ Failure Assessment (pSOFA). Categorical data were analyzed using Fisher's exact test, and a t-test was used for continuous variables. A two-sided p < 0.05 was considered significant.ResultsA total of 135 subjects were analyzed from the two cohorts. More patients were admitted during the PostLD phase (87 vs. 48). The PostLD group had a higher age at admission (11.2 ± 12.3 vs. 6.6 ± 7.5, p = 0.0075), but there were no differences in gender or race/ethnicity. The PostLD group also exhibited a higher proportion of RSV infections (73 vs. 16, p < 0.0001) and poly-viral infections (p < 0.0001). Higher coronavirus OC43 (9 vs. 0, p = 0.0263) and parainfluenza types 1-4 (human parainfluenza virus (HPIV)) (19 vs. 1, p = 0.0017) detections, yet fewer human metapneumovirus (HMPV) detections (0 vs. 4, p = 0.0147), were observed PostLD. No differences were found in hospital length of stay, PICU length of stay, mortality, mechanical ventilation days, ECLS days, or severity of illness scores based on PELOD-2 or pSOFA scores.ConclusionIn the bronchiolitis out-of-season surge, there were an increased number of admissions to the PICU. Those patients were older, and more likely to have RSV, as well as a coinfection with coronavirus OC43 or HPIV, yet less likely to have HMPV. No difference in length of stay or disease severity was demonstrated.

Intraoperative intracardiac thrombus in liver transplantation: A 9-year retrospective review focusing on treatment and outcomes.

This study characterizes incidence and outcomes surrounding intracardiac thrombosis (ICT) during liver transplantation over 9 years at a single center before and after the routine use of transesophageal echocardiography (TEE). Adult liver transplantation patients from 2011 to 2020 were divided into eras based on routine TEE use. ICTs were identified by querying anesthetic records for search terms. Descriptive statistics included counts and proportions for baseline recipient, donor, intraoperative, and postoperative characteristics. Outcome data were based on date of hospital discharge and date of death. The incidence of ICT increased in the TEE era (2016-2020) compared with the pre-TEE era (2011-2015; 3.7% [25/685] vs. 1.9% [9/491]; p < 0.001). Patients with ICT had significantly higher Model for End-Stage Liver Disease-sodium (MELD-Na) scores, pretransplant hospitalization, malignancy, drug-induced liver injury, hypertension, deep vein thrombosis, reperfusion syndrome, transfused platelets and cryoprecipitate, and use of hemostatic medications. A higher proportion of patients in the ICT group underwent simultaneous liver-kidney transplantation. The patients with ICT were similar, except patients in the pre-TEE era had higher MELD-Na scores and incidences of hepatitis C virus and lower incidences of encephalopathy. In the pre-TEE era, all ICTs presented as intraoperative cardiac arrest, and the 30-day mortality in the setting of ICT was 66.7% (6/9). During the TEE era, 80% of ICTs were diagnosed incidentally or attributed to hemodynamic instability (p=0.002). The 30-day mortality rate was 36% (9/25) in the TEE era (p=0.25). ICT incidence increased in the TEE era, yet the mortality rate was lower, suggesting that routine intraoperative TEE may lead to the early detection of ICT prior to hemodynamic collapse.

Rapid Treatment Initiation for Hepatitis C in Young People Who Inject Drugs: The Seek, Test, and Rapid Treatment Randomized Trial.

BackgroundYoung people who inject drugs (PWID) have high hepatitis C virus (HCV) incidence and low treatment initiation rates. Novel, simplified care models need to be developed to engage, treat, and cure hard-to-reach patient populations, such as young PWID. We present final data from the randomized pilot clinical trial “HCV-Seek Test and Rapid Treatment” for curing HCV in young PWID.MethodsParticipants were recruited from the community and eligible if they were 18–29 years of age, HCV antibody-positive, treatment naive, and had injected drugs in the past 30 days. Participants were randomized 1:1 to “Rapid Treatment or Usual Care”. Participants randomized to Rapid Treatment received same-day medical evaluation, confirmatory and baseline laboratory testing, and a 7-day starter pack of sofosbuvir/velpatasvir at a syringe service program (SSP). Participants in “Usual Care” received same-day HCV confirmatory testing at the SSP and, if positive, facilitated referral to local providers. The primary endpoint was sustained virologic response at 12 weeks (SVR12) in HCV ribonucleic acid (RNA)+ participant.ResultsForty-seven HCV antibody-positive participants were enrolled, and 25 participants had confirmed HCV and were included in the modified intention to treat analysis, with 9 of 14 (64%) of the Rapid Treatment arm and 1 of 11 (9.1%) of the Usual Care arm achieving a confirmed SVR12 (P = .01).ConclusionsAmong young HCV RNA+ PWID, significantly higher rates of cure were achieved using the Rapid Treatment model compared with facilitated referral. Providing easy access to HCV treatment for young PWID in low-threshold settings and initiating HCV treatment quickly appears to be a promising strategy for treating this hard-to-reach population.

Incidence and economic burden of respiratory syncytial virus among adults in the United States: A retrospective analysis using 2 insurance claims databases.

BACKGROUND: Respiratory syncytial virus (RSV) is a common, contagious, and seasonal pathogen causing 64 million acute respiratory infections annually in adults and children worldwide. High-risk adults, including older adults and those with cardiopulmonary conditions or weakened immune systems, are more likely to be infected. However, limited information exists on RSV incidence and associated costs among adults, including high-risk patients. OBJECTIVE: To evaluate the annual incidence of medically attended, International Classification of Diseases (ICD)-coded RSV among commercially insured adults and assess health care costs among adults with ICD-coded RSV in the United States. METHODS: Optum's deidentified Clinformatics Data Mart Database (January 01, 2007, to June 30, 2020) and IBM's MarketScan Databases (January 01, 2000, to July 31, 2020) were used. Medically attended, ICD-coded RSV incidence among adults was assessed from July 1 of a given year to June 30 of the next year and reported per 100,000 population. Trends in all-cause mean weekly costs pre-RSV and post-RSV diagnosis were reported. Results were reported overall and among patients aged 60-64 years, 65 years or older, 85 years or older, and 18-59 years at high risk of severe RSV (defined as having cardiopulmonary conditions or a weakened immune system). RESULTS: Annual incidence of medically attended, ICD-coded RSV in adults overall was 22.0-52.9 in Optum and 23.4-63.6 in MarketScan. Incidence rates were higher among patients aged 60-64 years (Optum: 25.2-66.1; MarketScan: 31.9-82.1), 65 years or older (Optum: 37.3-75.5; MarketScan: 54.1-97.3), 85 years or older (Optum: 92.4-140.6; MarketScan: 79.4-234.7), and 18-59 years at high risk of severe RSV (Optum: 41.3-135.9; MarketScan: 46.3-112.4). Mean weekly costs increased during the week before (Optum: $2,325; MarketScan: $2,080) and post-RSV diagnosis (Optum: $9,523; MarketScan: $3,551), compared with those in weeks 2-8 pre-RSV diagnosis (Optum: $1,350; MarketScan: $872). The increases in mean weekly costs during the week before and the week following RSV diagnosis were higher among patients aged 60-64 years (mean weekly costs in weeks 2-8 pre-RSV, week 1 pre-RSV, week 1 post-RSV; Optum: $1,623, $2,690, $10,823; MarketScan: $1,259, $2,992, $5,069), 65 years or older (Optum: $1,731, $3,067, $12,866; MarketScan: $1,517, $3,571, $5,268), 85 years or older (Optum: $1,563, $2,430, $18,134; MarketScan: $1,613, $4,113, $6,231), and 18-59 years at high risk of severe RSV (only for MarketScan: $1,237, $3,294, $5,531; costs were similar for Optum). CONCLUSIONS: Incidence of medically attended, ICD-coded RSV in adults was 22.0-63.6 per 100,000 population, a likely underestimation since RSV was not systematically tested and only RSV-coded cases were observed. Incremental costs associated with RSV were substantial. Incidence rates and costs were higher among patients aged 60 years or older and patients at high risk of severe RSV. DISCLOSURES: This study was sponsored by Janssen Scientific Affairs, LLC. The sponsor was involved in the study design, interpretation of results, manuscript preparation, and publication decisions. B. Brookhart and D. Anderson are employees of Janssen Scientific Affairs, LLC, and are stockholders of Johnson & Johnson. C. Rossi, B. Emond, J. Wang, P. Lefebvre, and M.-H. Lafeuille are employees of Analysis Group, Inc., a consulting company that has provided paid consulting services to Janssen Scientific Affairs, LLC, which funded the development and conduct of this study and manuscript. M. Mesa-Frias. and S. Drummond are former employees of Janssen Scientific Affairs, LLC. L. Lamerato is an employee of Henry Ford Health System and received research funding from Janssen Scientific Affairs, LLC.

Incidence and Severity of Aphid-transmitted Viruses and Horticultural Performance of Habanero Pepper (Capsicum chinense Jacq.) Breeding Lines in Benin

Habanero (Capsicum chinense Jacq.) is widely grown and consumed in West and Central African countries, and viral diseases represent an important production challenge. Diagnosis of the viral species affecting habanero productivity in Benin is limited, and understanding this will enable more efficient host resistance breeding. During 2019 and 2020, we characterized the incidence and severity of the viral diseases infecting nine promising habanero breeding lines and one commercial hybrid check under open field conditions in Benin. The horticultural performance, including yield and yield component traits of the entries, was determined during the 2 years of the experiment. A randomized complete block design was used with three replications, each with 24 plants. Data were recorded on days to 50% flowering and 50% fruit maturity, yield and on the yield components of fruit weight (g), fruit length (cm), and fruit width (mm), as well as disease incidence and severity. In total, 35 leaf samples were collected for viral diagnosis among habanero breeding lines. We found that Pepper veinal mottle virus (PVMV; Potyvirus) was the overwhelmingly predominant virus in our trials, with an 80% incidence; however, we found frequent coinfection of PVMV with Cucumber mosaic virus (CMV, Cucumovirus), Polerovirus, and, to a lesser extent, Chili veinal mottle virus (ChiVMV; Potyvirus). The mean disease incidence across all entries was 60%. AVPP1932 and PBC 2010 had the lowest disease incidence (35% and 43%, respectively), whereas AVPP1929 had the highest (86%) disease incidence. The F1 hybrid check Afadja had the overall highest yield, with 30 t⋅ha−1, followed by AVPP1932, with 19 t⋅ha−1, both in 2019. There was a negative correlation between disease incidence and total yield (r = −0.44; P &lt; 0.001), supporting previous studies indicating that viral diseases are major production constraints for habanero in West Africa. This study provides insight regarding the need to improve habanero for resistance to aphid-transmitted viruses and develop integrated pest management strategies to limit losses in Benin.

Hepatitis C incidence among patients attending primary care health services that specialise in the care of people who inject drugs, Victoria, Australia, 2009 to 2020.

Monitoring trends in hepatitis C virus (HCV) incidence is critical for evaluating strategies aimed at eliminating HCV as a public health threat. We estimate HCV incidence and assess trends in incidence over time among primary care patients. Data were routinely extracted, linked electronic medical records from 12 primary care health services. Patients included were aged ≥16 years, tested HCV antibody negative on their first test recorded and had at least one subsequent HCV antibody or RNA test (January 2009-December 2020). HCV incident infections were defined as a positive HCV antibody or RNA test. A generalised linear model assessed the association between HCV incidence and calendar year. In total, 6711 patients contributed 17,098 HCV test records, 210 incident HCV infections and 19,566 person-years; incidence was 1.1 per 100 person-years (95% confidence interval (CI): 0.9 to 1.2). Among 559 (8.2%) patients ever prescribed opioid-related pharmacotherapy (ORP) during the observation period, 135 infections occurred during 2,082 person-years (incidence rate of 6.5 per 100 person-years (95% CI: 5.4 to 7.7)). HCV incidence declined 2009-2020 overall (incidence rate ratio per calendar year 0.8 (95% CI: 0.8 to 0.9) and among patients ever prescribed ORT (incidence rate ratio per calendar year 0.9, 95% CI: 0.75 to 1.0). HCV incidence declined among patients at primary care health services including among patients ever prescribed ORP and during the period following increased access to DAA therapy.

Investigating the effects of planting date and Aphis gossypii management on reducing the final incidence of cotton leafroll dwarf virus

This is the first study to research management strategies for cotton leafroll dwarf virus (CLRDV) in the southeastern U.S. The efficacy of aphid vector management to reduce final CLRDV incidence was investigated concurrent with efforts to monitor aphid population dynamics and timing of CLRDV spread. Adjusting the planting date and insecticide applications did not reduce the final incidence of CLRDV, which was confirmed in 60–100% of plants per plot using RT-PCR. Aphid population density was reduced, but not eliminated with foliar insecticide applications. Aphis gossypii was the only species observed on cotton and was the dominant species collected in pan traps. Three distinct periods of virus spread were detected with sentinel plants including early, mid-and late-season. Most virus spread occurred during large aphid dispersal events.

Combining Cultural Tactics and Insecticides for the Management of the Sweetpotato Whitefly, Bemisia tabaci MEAM1, and Viruses in Yellow Squash

The sweetpotato whitefly, Bemisia tabaci MEAM1 Gennadius (Hemiptera: Aleyrodidae), and the complex of viruses it transmits are major limiting factors to squash production in the southeastern United States. At this time, insecticides are extensively relied upon for the management of whiteflies and, indirectly, whitefly-transmitted viruses. The development of a multi-faceted, integrated pest management (IPM) program is needed to increase the sustainability and profitability of squash production. Experiments in 2018 and 2019 evaluated the effects of insect exclusion netting (IEN) in combination with selected pesticides on whitefly population dynamics and virus incidence in greenhouse-grown squash seedlings. Field experiments from 2018 to 2021 evaluated the effects of mulch type (UV-reflective mulch, live mulch, and white plastic mulch), row covers, and insecticides on whitefly population dynamics, silver leaf disorder (SSL) intensity, virus symptom severity, and marketable yield. IEN significantly reduced whiteflies and virus incidence on squash seedlings in the greenhouse study. In the field mulch study, lower whitefly abundance and SSL intensity, as well as reduced virus symptom severity, were observed in plots with reflective mulch compared with white plastic or live mulch. In the insecticide/row cover study, whitefly abundance, SSL intensity, and virus symptom severity were lowest in the row cover and cyantraniliprole- and flupyradifurone-treated plots. Field plots with row covers and those with UV-reflective mulch consistently produced the greatest marketable yields. These findings demonstrate that growers can reduce whitefly and virus pressure and preserve yields in squash production in the southeastern United States by combining cultural and chemical tactics, including row covers, UV-reflective mulch, and select insecticides.

Spatial Roguing Reduces the Incidence of Leafroll Disease and Curtails Its Spread in a Finger Lakes Cabernet franc Vineyard

<h3>Abstract</h3> Leafroll is one of the most economically important viral diseases of grapevines worldwide. Grapevine leafroll-associated virus 1 (GLRaV-1) and grapevine leafroll-associated virus 3 (GLRaV-3) are prevalent in New York vineyards in which low-density grape mealybug populations reside. A five-year experiment was performed in a commercial ‘Cabernet franc’ vineyard in the Finger Lakes region of New York to test the influence of spatial roguing, i.e., the elimination of virus-infected vines and their two immediate within-row neighbors on each side, on the annual incidence of GLRaV-1 and GLRaV-3. In a second treatment, spatial roguing was combined with insecticides. Vines eliminated in both spatial roguing treatments were replaced by clean vines derived from virus-tested stocks. The objective of this study was to reduce temporal virus incidence to less than 1% over two consecutive years and limit virus spread. In both spatial roguing treatments, virus incidence was reduced from 5% in 2016 to less than 1% in 2020-2021. Among vines in the insecticide-free, non-rogued control treatment, virus incidence increased from 5% to 16% from 2016 to 2021. Insecticides applied in 2016-2021 helped significantly reduce grape mealybug populations to near zero annually, while populations in the untreated control vines were 57 to 257-fold higher during the same period. However, insecticides contributed relatively little to limit the number of newly infected vines. Together, these findings highlight the salient contribution of roguing to an overall leafroll disease management response in a vineyard with low disease incidence and low grape mealybug abundance. To our knowledge, this is the first report on the effectiveness of spatial roguing at reducing the annual incidence of leafroll disease in a vineyard.

HIV epidemic in a province of the Brazilian Amazon region: Temporal trend analysis.

BackgroundAlthough considerable progress has been made over the last decades, human immunodeficiency virus (HIV) incidence and acquired immunodeficiency syndrome (AIDS) mortality rates have remarkably increased in the Brazilian Amazon region. Here, we employed temporal analysis to determine the impact of public policies on the HIV epidemic in the state of Pará, Brazil, which has the second highest HIV incidence rate in the Amazon region.Design and methodsThis is an ecological study conducted in the state of Pará, employing secondary data of HIV/AIDS cases notified to the Information System for Notifiable Diseases, 2007– 2018. The following epidemiological variables were collected: year of notification, municipality of residence, age, sex, education, exposure category, and HIV/AIDS diagnostic criteria. The study population was composed of 21,504 HIV/AIDS cases. The HIV/AIDS incidence rates were analyzed employing the temporal trend analysis (TTA) followed by the chi-square test and residue analysis to determine the association between the epidemiological variables and time series periods.ResultsA total of 50% of the notifications were composed of AIDS cases. TTA identified two periods in HIV/AIDS incidence, with stabilization of cases in the first period (G1, 2007–2012) and an upward trend in the second period (G2, 2012–2018). The most prevalent epidemiological characteristics in G2 (versus G1) were as follows: young people, brown skin color, higher schooling, and homosexuals.ConclusionsPublic policy to control HIV infection in the Brazilian Amazon region has been partially effective. HIV screening tests and treatment should be made widely available to eradicate HIV infection in the Amazon region by 2030.

Incidence and Distribution of Barley yellow dwarf virus Infecting Oats in Korea

A survey of Barley yellow dwarf virus (BYDV) was conducted in major oat-growing areas of Korea in 2020. BYDV is an economically important pathogen of cereal crops that can be transmitted by aphids. The present study evaluated the genetic composition of BYDV in oat from eight geographical areas in Korea. Multiplex reverse transcription-polymerase chain reaction was used to screen 322 oat leaf samples for six BYDV strains (PAV, MAV, SGV, PAS, RPV, and RMV). The 125 samples (~39%) tested positive for BYDV. BYDV-PAV, BYDV-SGV, BYDV-PAS, and BYDV-RPV were detected from oat in different areas. Most of the BYDV-infected samples were assigned to subgroup I (n=112). The results indicate that BYDV-PAV could be dominant throughout Korea. Also, the phylogenetic analysis of coat protein sequences indicated that 23 BYDV isolates from Korea could be separated into two clades, which exhibited high nucleotide sequence similarity. In conclusion, the present survey provides a BYDV infection assessment for domestic oat varieties in Korea and basic information for the development of BYDV control measures in Korea’s oat industry.

Apple cultivars and rootstocks assay for the identification of diverse viruses and healthy genotypes for breeding

The prevalence of harmful viruses, viz., apple stem grooving virus (ASGV), apple stem pitting virus (ASPV), apple chlorotic leaf spot virus (ACLSV), apple mosaic virus (ApMV), and tomato ringspot virus (ToRSV) in apple tree plantations in the Ryazan, Yaroslavl, and Moscow regions, Russian Federation, based on genotype features, planting type (industrial, collection, and repository), and tree age was studied during 2018–2021. The prevalence of harmful and latent viruses ranged from 49.6% to 53.8% in apple cultivars and from 8.3% to 100% in apple clonal rootstocks. The most common virus in the Moscow and Yaroslavl regions was ACLSV (34.7% and 53.8%) and that in the Ryazan region was ApMV (33.3%). Relative to that in young apple trees, the virus influence in older tree tissues was higher by 20% to 43% depending on virus type. Monoviral infection prevailed (59% of all trees were infected with one virus) in the studied apple tree cultivars. Of the cultivars, 25% were infected by a complex of two viruses (ASPV + ACLSV), 10% were infected by three viruses, and 6% were infected by four viruses. The highest prevalence of latent viruses was observed in old Russian cultivars (53.5%) and selections from old foreign cultivars (57.2%). Virus occurrence was slightly lower (51.6%) in new Russian cultivars than in other cultivars. Columnar apple tree cultivars had the lowest virus occurrence (30%) and were found to be more tolerant than other genotypes. The highest virus incidence was recorded in industrial orchards (63.4%), followed by that recorded in collection (20.8%) and repository (18.3%) plantations. By using ELISA, the apple genotypes that were free from harmful viruses were identified as source plants, i.e., 183 plants from 18 apple tree cultivars and 131 plants from clonal rootstocks. Results indicated that virus-free apple germplasm is highly effective for the successful implementation of breeding and genetic improvement.

Analyses of Kaposi Sarcoma trends among adults establishing initial outpatient HIV care in Nigeria: 2006\u20132017

BackgroundThe incidence of Human Immunodeficiency Virus (HIV)-associated Kaposi Sarcoma (KS) in the pre-antiretroviral therapy (ART) population remains high in several countries in sub-Saharan Africa. We examined trends of KS prevalence in adults, establishing initial outpatient HIV care from 2006 to 2017 in Nigeria.MethodsWe analyzed data of 16,431 adults (age ≥ 18 years) enrolled for HIV care from January 1, 2006, to December 31, 2017, in a large clinic in Jos, Nigeria. KS at enrollment was defined as KS recorded in the electronic health record within 30 days of clinic enrollment. Time trends were compared among four periods: 2006–2008, 2009–2011, 2012–2014, and 2015–2017 using logistic regression models. Annual trends were analyzed using join point regression and restricted splines.ResultsThe study population had a mean age 35.1 (standard deviation, SD 9.5) years, and were 65.7% female (n = 10,788). The mean CD4 cell count was 220 (95% CI 117–223). The overall KS prevalence at entry was 0.59% (95% CI 0.48–0.72). Compared to 2006–2008, KS prevalence was significantly higher in 2009–2011 (adjusted odds ratio 5.07 (95% CI 3.12–8.24), p < 0.001), but remained unchanged in subsequent periods. Male sex and low CD4 T-cell count independently increased odds for KS.ConclusionsDespite ART expansion, KS at enrollment showed no significant decline. The low CD4 cell count, across all periods, indicates delay in enrollment for HIV care, which increases KS risk. Interventions aimed at early HIV diagnosis and linkage to ART is critical to KS risk reduction in this population.

Epidemiological Characteristics and the Development of Prognostic Nomograms of Patients With HIV-Associated Cutaneous T-Cell Lymphoma.

BackgroundThe incidence of human immunodeficiency virus (HIV) associated cutaneous T-Cell lymphoma (HIV-associated CTCL) is very low, and there is a lack of relevant epidemiological and clinical prognostic studies. Therefore, we aimed to study the epidemiological characteristics of HIV-associated CTCL and to construct and validate a nomogram predicting patient survival.MethodsDemographic, clinical characteristics, and incidence data from the Surveillance, Epidemiology and End Results (SEER) database were screened for patients with HIV-associated CTCL. Independent prognostic factors in patients with HIV-associated CTCL were analyzed to establish nomograms of overall survival (OS) and disease-specific survival (DSS) rates of patients. The performance of the prediction model was validated by the consistency index (C-index), the area under the receiver operating characteristic curve (AUC), and calibration plots.ResultsA total of 883 eligible patients were screened for inclusion in this study and randomized to the training cohort (70%, n = 619) and the validation cohort (30%, n = 264). The age-adjusted average incidence rate per 100,000 persons per year for HIV-associated CTCL was 0.071 for the period 2004-2017, with an increasing incidence rate. The median age of the included patients was 59 years, of which male Caucasian held a majority. 99.5% of the patients had a tumor tissue subtype of mycosis fungoides, while the other tumor subtypes were sézary syndrome. The median OS for patients with HIV-associated CTCL was 162 months, and the OS rates at 1, 3, 5, and 10 years were 0.964, 0.904, 0.835, and 0.766, respectively. Univariate and multivariate COX regression analysis were performed, and prognostic indicators such as “Age”, “Radiation”, “Chemotherapy”, “Summary stage”, “Sequence number” were ultimately incorporated and used to establish nomograms of OS and DSS rates at 1, 3, 5 and 10 years for the training cohort. The C-index, AUC, and calibration plot confirmed that our prediction model had good accuracy.ConclusionWhile HIV-associated CTCL is very rare, its incidence has been on the rise in the last decade or so. We described the epidemiological characteristics and prognostic factors in patients with HIV-associated CTCL.

The Optimization of HIV Testing in Eastern Indonesia: Findings from the 2017 Indonesian Demographic and Health Survey.

There is a concerning increase in human immunodeficiency virus (HIV) incidence in eastern Indonesia. HIV testing rates in this area are the lowest in the country. This study aimed to analyze the determinants of HIV testing in the Public Health Centers (PHCs) in eastern Indonesia. A cross-sectional study design was utilized using secondary data from the 2017 Indonesian Demographic and Health Survey (IDHS). We focused the survey on eastern Indonesia (Sulawesi, Maluku, and Papua) with PHC settings. After we weighted and removed missing data, we obtained 2118 surveys (425 males and 1693 females aged 14–54 years). Chi-square and binary logistic regression were used to analyze the determinants of HIV testing optimization in eastern Indonesia with a significance level of p < 0.05. The HIV testing coverage at the PHCs in eastern Indonesia was found to be 28.28%. From the survey, we found that respondents from the province of Papua (AOR: 1.45; 95% CI: 1.09–1.91), those who were female (AOR: 2.37; 95% CI: 1.75–3.12), and those with more information on HIV (AOR: 1.88; 95% CI: 1.41–2.51) were more likely to undergo HIV testing at the PHCs. Meanwhile, the wealthiest respondents (AOR: 0.61; 95% CI: 0.42–0.89) and the respondents who engaged in the perpetuation of stigmatization (AOR: 0.65; 95% CI: 0.42–1.02) were less likely to undergo HIV testing at the PHCs. The coverage of HIV testing in eastern Indonesia needs special attention from the Indonesian government. Increasing equity, distributing information regarding HIV and acquired immunodeficiency syndrome (AIDS) through social media, and creating accessible HIV testing in rural areas are vital for developing appropriate interventions.

The Establishment and Spread of a Newly Introduced Begomovirus in a Dry Tropical Environment Using Tomato Yellow Leaf Curl Virus as a Case Study.

Early detection of tomato yellow leaf curl virus (TYLCV) in a previously unaffected tomato production district in Australia allowed its spread to be evaluated spatially and temporally. The population dynamics of the TYLCV vector, Bemisia argentifolii (silverleaf whitefly, SLW), were also evaluated. The district is a dry tropical environment with a clear break to commercial production during the summer wet season. The incidence of TYLCV within crops and its prevalence through the district was influenced by weather, location, vector movements, and the use of Ty-1 virus-resistant hybrids. Rainfall had an important influence, with late summer and early autumn rain suppressing the levels of SLW and, by contrast, a dry summer supporting faster population growth. The use of Ty-1 hybrids appears to have reduced the incidence of TYLCV in this district. There was limited use of Ty-1 hybrids during 2013, and by season end, crops had moderate levels of SLW and high virus incidence. The 2015 and early 2016 season had high SLW populations, but TYLCV incidence was lower than in 2013, possibly due to the widespread adoption of the Ty-1 hybrids reducing virus spread. This study provides valuable epidemiology data for future incursions of begomoviruses, and other viruses spread by SLW.

First Report of Garlic virus A, Garlic virus B, and Garlic virus C on Garlic (Allium sativum) in Tunisia.

Mite-borne viruses belonging to the genus Allexivirus (family Alphaflexiviridae) commonly occur on garlic in many parts of the world. There are usually asymptomatic and cause small damage to the plants, but often occur in mixed infection with potyviruses and carlaviruses, with synergistic effects reducing crop quality and leading to higher losses (Taglienti et al. 2017). Their occurrence on Tunisian garlic crops was studied here in the same garlic germplasm collection mentioned in a previous first report (Ayed et al. 2019). Leaf samples from a total of 66 garlic accessions were tested by DAS-ELISA using specific antibodies (DSMZ, Germany) against garlic virus A (GarV-A), garlic virus B (GarV-B) and garlic virus C (GarV-C). These serological tests showed individual virus incidence of respectively 56.4%, 67.7% and 10%. Our findings corroborate with the results of Chodorska et al (2012). In order to confirm the presence of these viruses, RT-PCR assays were performed using total RNAs extracted using two silica-capture extraction procedures according to Foissac et al (2005) and specific primers targeting the coat protein genes of the various viruses. These primers, designed for the present study are (GarV-A-F: 5' YCTYTTCTCHYTDGCHTGGACYTG 3' and GarV-A-R: 5' RCCYTTCCTAGACCARTTRGCRGG 3' for GarV-A; GarV-B-F: 5' TGGGCYTGYTACCACAAYGGATC 3' and GarV-B-R 5' TCTGCGCGVGTGGADACCATRTT 3' for GarV-B; GarV-C-F: 5' ARGAYCTYTTYTCMCTYGCRTGGGC 3' and GarV-C-R: 5' GGAGGYTCRTGAATYTGTTGTTG 3' for GarV-C). The viruses were detected by a two-step RT-PCR as described by Marais et al (2015). PCRs consisted of one cycle at 95 °C for 5 min; followed by 40 cycles of denaturation at 95 °C for 45 s, annealing at 45 °C for 45 s, and elongation at 72 °C for 45s; and a final extension step at 72 °C for 10 min. Products of the expected size (214 bp for GarV-A, 363 bp for GarV-B and 439 bp for GarV-C) were amplified from 58 (88%), 47 (71%) and 56 (85%) accessions, respectively. Forty three samples (65%) were co-infected by the three viruses. Higher numbers of positives revealed by RT-PCR especially in the case of GarV-C may reflect the higher sensitivity and efficiency of this technique compared to ELISA. Direct sequencing of selected amplicons of the expected size obtained for GarV-A, -B, and -C Tunisian isolates was performed and the sequences submitted to GenBank, validating the specificity of the three RT-PCR assays. The two sequenced GarV-A isolates (MK599147 and MN995836) shared 98% nucleotide (nt) sequence identity with each other, and 93-94% identity with the closest isolate in GenBank, the "G118" isolate from China (MN059320). The three sequenced GarV-B isolates (MN995829 to MN995831) shared 88-98% nt identity with each other. For "GarV-B 18.1" (MN995830) and "GarV-B 36.2" (MN995831) the closest isolate was "1109.1" (JX682828) from Spain (92-93% nt identity). For "GarVB 17.2" (MN995829), the closest isolate was "B-Sp-3" (LC97167) from Spain (90% nt identity). The sequenced GarV-C isolate (MN995834) showed the highest sequence nt identity (93%) with the "GarV-9" isolate (HQ724848) from Spain. To our knowledge this is the first report of the presence of GarV-A, -B and -C in Tunisia. The presence of these allexiviruses may pose a threat to the preservation of the Tunisian garlic germplasm and, more broadly, to garlic production in Tunisia. For this reason, the scrupulous identification of viruses occurring in garlic plants will help to use the appropriate strategy to decrease viral incidence in garlic growing area.