Last data update: Jan 27, 2025. (Total: 48650 publications since 2009)
Records 1-30 (of 32 Records) |
Query Trace: Deyde V[original query] |
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COVID-19 clinical characteristics and outcomes in children and adolescents hospitalized at the university hospital of the west indies, Jamaica in 2020-2021 (preprint)
Berry CLS , Melbourne-Chambers RH , Harrison AN , Anzinger JJ , Gordon-Johnson KAM , Deyde VM , Christie CDC . medRxiv 2021 28 Background and Objectives: Multisystem inflammatory syndrome of children (MISC) carries a high attributable morbidity. We describe children aged <16 years hospitalised with COVID-19 and/or MISC, April 2020 to June 2021. Method(s): All were tested for SARS-CoV-2, infectious disease consultations performed, modified CDC criteria for MISC applied, charts reviewed and data analyzed. Result(s): Among 79 consecutive children with SARS-CoV-2, 41(52%) were hospitalised; with median age 10.5 years; Afro-Caribbean ethnicity 40(98%); males 21(51%); SARS-CoV-2 RT-PCR positivity 26 (63%), IgG/IgM positivity 7(17%), community exposures 8 (20%). MISC-cases 18 (44%) vs. non-MISC 23(56%) had fever (94% vs. 30%; p<0.01), fatigue/lethargy (41% vs. 4%; p=0.004), rhinorrhoea (28% vs. 4%; p=0.035), elevated neutrophils (100% vs. 87%; p=0.024) and >=4 abnormal inflammatory biomarkers 13 (72%). MISC-cases had >2 organ/systems (100% vs. 35%; p<0.01), including gastrointestinal (72% vs. 17%; p<0.01), haematological/coagulopathic (67% vs. 4%; p<0.01); dermatologic (56% vs. 0%; p<0.01), cardiac (17% vs. 0%; p=0.042) with Kawasaki Syndrome (44% vs. 0%; p<0.01) and pleural effusions (17% vs. 0%; p=0.042). MISC-cases were treated with intravenous immune gammaglobulin (14, 78%), aspirin (12, 68%), steroids (9, 50%) and intensive care with non-invasive ventilation (2, 11%). One (6%) with pre-morbid illness died, the remainder recovered. Conclusion(s): MISC was treated successfully with intravenous gammaglobulin, steroids and/or aspirin in 94% before cardiopulmonary decompensation, or need for inotropes, vasopressors, or invasive ventilation. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license. |
Hospitalized children with SARS-CoV-2 infection and MIS-C in Jamaica: A dive into the first 15 months of the novel pandemic
Berry CS , Melbourne-Chambers RH , Harrison AN , Anzinger JJ , Gordon-Johnson KM , Deyde VM , Christie CDC . Front Pediatr 2022 10 904788 OBJECTIVES: COVID-19 in children was initially mild until the emergence of Multisystem Inflammatory Syndrome in Children (MIS-C). We describe pediatric COVID-19 in a developing country within the Caribbean. METHODS: Jamaican children who were hospitalized with SARS-CoV-2 infection, in one Caribbean regional academic referral center from April 2020 through June 2021 were included. Prospective surveillance and pediatric infectious disease consultations were performed using the CDC's MIS-C case definition. Data were extracted from patients' hospital charts using WHO's reporting form, entered into the RedCap database, and SPSS 28 was used for analysis. MIS-C and non-MIS-C patients were compared using independent sample t-tests for continuous variables and Fisher's exact test for categorical variables, p values < 0.05 were statistically significant. RESULTS: Seventy-nine children with COVID-19 with/without MIS-C presented to UHWI. Thirty-eight (48%) were mild ambulatory cases. Hospitalizations occurred in 41 (52%) children, with median age of 10 ½ years. SARS-CoV-2 RT-PCR positivity was present in 26 (63%), Immunoglobulin M, or Immunoglobulin G (IgM/IgG) positivity in 8 (20%), with community exposures in 7 (17%). Eighteen (44%) MIS-C positive patients were significantly more likely than 23 MIS-C negative patients (56%) to present with fever (94% vs. 30%; p < 0.001), fatigue/lethargy (41% vs. 4%; p = 0.006), lymphadenopathy (33% vs. 0%; p = 0.003), elevated neutrophils (100% vs. 87%; p = 0.024), and ESR (78% vs. 9%; p = 0.002). Involvement of > two organ systems occurred more frequently in MIS-C positive cases (100% vs. 34%; p < 0.001), including gastrointestinal (72% vs. 17%; p < 0.001); vomiting/nausea (39% vs. 9%; p < 0.028); hematological/coagulopathic (67% vs. 4%; p < 0.001); dermatologic involvement (56% vs. 0%; p < 0.001); and mucositis (28% vs. 0%; p = 0.001). MIS-C patients had Kawasaki syndrome (44%), cardiac involvement (17%), and pleural effusions (17%). MIS-C patients had >4 abnormal inflammatory biomarkers including D-dimers, C-reactive protein, ESR, ferritin, troponins, lactate dehydrogenase, neutrophils, platelets, lymphocytes, and albumen (72%). MIS-C patients were treated with intravenous immune gamma globulin (78%), aspirin (68%), steroids (50%), and non-invasive ventilation (11%). None required inotropes/vasopressors. MIS-C negative patients received standard care. All recovered except one child who was receiving renal replacement therapy and developed myocardial complications. CONCLUSIONS: In this first report of COVID-19 from the Caribbean, children and adolescents with and without MIS-C were not very severe. Critical care interventions were minimal and outcomes were excellent. |
Prevalence of drug-resistant tuberculosis and imputed burden in South Africa: a national and sub-national cross-sectional survey
Ismail NA , Mvusi L , Nanoo A , Dreyer A , Omar SV , Babatunde S , Molebatsi T , van der Walt M , Adelekan A , Deyde V , Ihekweazu C , Madhi SA . Lancet Infect Dis 2018 18 (7) 779-787 BACKGROUND: Globally, per-capita, South Africa reports a disproportionately high number of cases of multidrug-resistant (MDR) tuberculosis and extensively drug-resistant (XDR) tuberculosis. We sought to estimate the prevalence of resistance to tuberculosis drugs in newly diagnosed and retreated patients with tuberculosis provincially and nationally, and compared these with the 2001-02 estimates. METHODS: A cross-sectional survey was done between June 15, 2012-June 14, 2014, using population proportionate randomised cluster sampling in the nine provinces in South Africa. 343 clusters were included, ranging between 31 and 48 per province. A patient was eligible for inclusion in the survey if he or she presented as a presumptive case during the intake period at a drug resistance survey enrolling facility. Consenting participants (>/=18 years old) completed a questionnaire and had a sputum sample tested for resistance to first-line and second-line drugs. Analysis was by logistic regression with robust SEs, inverse probability weighted against routine data, and estimates were derived using a random effects model. FINDINGS: 101 422 participants were tested in 2012-14. Nationally, the prevalence of MDR tuberculosis was 2.1% (95% CI 1.5-2.7) among new tuberculosis cases and 4.6% (3.2-6.0) among retreatment cases. The provincial point prevalence of MDR tuberculosis ranged between 1.6% (95% CI 0.9-2.9) and 5.1% (3.7-7.0). Overall, the prevalence of rifampicin-resistant tuberculosis (4.6%, 95% CI 3.5-5.7) was higher than the prevalence of MDR tuberculosis (2.8%, 2.0-3.6; p=0.01). Comparing the current survey with the previous (2001-02) survey, the overall MDR tuberculosis prevalence was 2.8% versus 2.9% and prevalance of rifampicin-resistant tuberculosis was 3.4% versus 1.8%, respectively. The prevalence of isoniazid mono-resistant tuberculosis was above 5% in all provinces. The prevalence of ethionamide and pyrazinamide resistance among MDR tuberculosis cases was 44.7% (95% CI 25.9-63.6) and 59.1% (49.0-69.1), respectively. The prevalence of XDR tuberculosis was 4.9% (95% CI 1.0-8.8). Nationally, the estimated numbers of cases of rifampicin-resistant tuberculosis, MDR tuberculosis, and isoniazid mono-resistant tuberculosis for 2014 were 13 551, 8249, and 17 970, respectively. INTERPRETATION: The overall prevalence of MDR tuberculosis in South Africa in 2012-14 was similar to that in 2001-02; however, prevalence of rifampicin-resistant tuberculosis almost doubled among new cases. Furthermore, the high prevalence of isoniazid mono-resistant tuberculosis, not routinely screened for, and resistance to second-line drugs has implications for empirical management. FUNDING: President's Emergency Plan for AIDS Relief through the Centers for Disease Control and Prevention under the terms of 1U19GH000571. |
New biomarkers of innate and adaptive immunity in infectious diseases
Morzunov S , Deyde V , Abrahamyan L . J Immunol Res 2017 2017 7047405 Despite dramatic achievements in the field of infectious disease control and prevention in economically developed countries, infectious diseases still remain the leading cause of morbidity, disability, and mortality worldwide. According to the World Health Organization (WHO), 15 million fatalities were attributed to infectious diseases in 2010. It is extremely alarming that the WHO predicts 13 million infectious disease-related deaths for 2050 [1]. In particular, emerging infectious diseases are on the rise, which can be explained by many factors like microbial adaptation to new hosts, selective pressures of the treatment, migration of the natural hosts, and so on. Emerging infectious diseases often have deadly consequences which may threaten the existence of humanity. Although much has been learnt about the pathogenesis of infectious diseases, reliable early diagnosis and effective treatment for many of these diseases are still not available. These limitations could be explained by our limited knowledge of the molecular host-pathogen interactions and immune response to many particular infections, which hampers the discovery of the early diagnostic biomarkers. |
Virologic outcome among patients receiving antiretroviral therapy at five hospitals in Haiti
Jean Louis F , Buteau J , Francois K , Hulland E , Domercant JW , Yang C , Boncy J , Burris R , Pelletier V , Wagar N , Deyde V , Lowrance DW , Charles M . PLoS One 2018 13 (1) e0192077 INTRODUCTION: Viral load (VL) assessment is the preferred method for diagnosing and confirming virologic failure for patients on antiretroviral therapy (ART). We conducted a retrospective cross-sectional study to evaluate the virologic suppression rate among patients on ART for >/=6 months in five hospitals around Port-au-Prince, Haiti. METHODS: Plasma VL was measured and patients with VL <1,000 copies/mL were defined as virologically suppressed. A second VL test was performed within at least six months of the first test. Factors associated with virologic suppression were analyzed using logistic regression models accounting for site-level clustering using complex survey procedures. RESULTS: Data were analyzed for 2,313 patients on ART for six months or longer between July 2013 and February 2015. Among them, 1,563 (67.6%) achieved virologic suppression at the first VL test. A second VL test was performed within at least six months for 718 (31.0%) of the patients. Of the 459 patients with an initial HIV-1 RNA <1,000 copies/mL who had a second VL performed, 394 (85.8%) maintained virologic suppression. Virologic suppression was negatively associated with male gender (adjusted odds ratio [aOR]: 0.80, 95% CI: 0.74-0.0.86), 23 to 35 months on ART (aOR:0.72[0.54-0.96]), baseline CD4 counts of 201-500 cells/mm3 and 200 cells/mm3 or lower (aORs: 0.77 [0.62-0.95] and 0.80 [0.66-0.98], respectively), poor adherence (aOR: 0.69 [0.59-0.81]), and TB co-infection (aOR: 0.73 [0.55-0.97]). CONCLUSIONS: This study showed that over two-thirds of the patients in this evaluation achieved virologic suppression after >/= six months on ART and the majority of them remained suppressed. These results reinforce the importance of expanding access to HIV-1 viral load testing in Haiti for monitoring ART outcomes. |
Trends in tuberculosis case notification and treatment success, Haiti, 2010-2015
Charles M , Richard M , Joseph P , Bury MR , Perrin G , Louis FJ , Fitter DL , Marston BJ , Deyde V , Boncy J , Morose W , Pape JW , Lowrance DW . Am J Trop Med Hyg 2017 97 49-56 Since the 2010 earthquake, tuberculosis (TB) control has been a major priority for health sector response and recovery efforts in Haiti. The goal of this study was to analyze trends in TB case notification in Haiti from the aggregate data reported by the National TB Control Program to understand the effects of such efforts. A total of 95,745 TB patients were registered for treatment in Haiti between 2010 and 2015. Three regions, the West, Artibonite, and North departments accounted for 68% of the TB cases notified during the period. Patients in the 15-34 age groups represented 53% (50,560) of all cases. Case notification rates of all forms of TB increased from 142.7/100,000 in 2010 to 153.4 in 2015, peaking at 163.4 cases/100,000 in 2013. Case notification for smear-positive pulmonary TB increased from 85.5 cases/100,000 to 105.7 cases/100,000, whereas treatment success rates remained stable at 79-80% during the period. Active TB case finding efforts in high-risk communities and the introduction of new diagnostics have contributed to increasing TB case notification trends in Haiti from 2010 to 2015. Targeted interventions and novel strategies are being implemented to reach high-risk populations and underserved communities. |
Building and rebuilding: The national public health laboratory systems and services before and after the earthquake and cholera epidemic, Haiti, 2009-2015
Jean Louis F , Buteau J , Boncy J , Anselme R , Stanislas M , Nagel MC , Juin S , Charles M , Burris R , Antoine E , Yang C , Kalou M , Vertefeuille J , Marston BJ , Lowrance DW , Deyde V . Am J Trop Med Hyg 2017 97 21-27 Before the 2010 devastating earthquake and cholera outbreak, Haiti's public health laboratory systems were weak and services were limited. There was no national laboratory strategic plan and only minimal coordination across the laboratory network. Laboratory capacity was further weakened by the destruction of over 25 laboratories and testing sites at the departmental and peripheral levels and the loss of life among the laboratory health-care workers. However, since 2010, tremendous progress has been made in building stronger laboratory infrastructure and training a qualified public health laboratory workforce across the country, allowing for decentralization of access to quality-assured services. Major achievements include development and implementation of a national laboratory strategic plan with a formalized and strengthened laboratory network; introduction of automation of testing to ensure better quality of results and diversify the menu of tests to effectively respond to outbreaks; expansion of molecular testing for tuberculosis, human immunodeficiency virus, malaria, diarrheal and respiratory diseases; establishment of laboratory-based surveillance of epidemic-prone diseases; and improvement of the overall quality of testing. Nonetheless, the progress and gains made remain fragile and require the full ownership and continuous investment from the Haitian government to sustain these successes and achievements. |
Retention throughout the HIV care and treatment cascade: from diagnosis to antiretroviral treatment of adults and children living with HIV-Haiti, 1985-2015
Auld AF , Valerie Pelletier , Robin EG , Shiraishi RW , Dee J , Antoine M , Desir Y , Desforges G , Delcher C , Duval N , Joseph N , Francois K , Griswold M , Domercant JW , Patrice Joseph YA , Van Onacker JD , Deyde V , Lowrance DW , The Groupe d'Analyses Salvh . Am J Trop Med Hyg 2017 97 57-70 Monitoring retention of people living with HIV (PLHIV) in the HIV care and treatment cascade is essential to guide program strategy and evaluate progress toward globally-endorsed 90-90-90 targets (i.e., 90% of PLHIV diagnosed, 81% on sustained antiretroviral therapy (ART), and 73% virally suppressed). We describe national retention from diagnosis throughout the cascade for patients receiving HIV services in Haiti during 1985-2015, with a focus on those receiving HIV services during 2008-2015. Among the 266,256 newly diagnosed PLHIV during 1985-2015, 49% were linked-to-care, 30% started ART, and 18% were retained on ART by the time of database closure. Similarly, among the 192,187 newly diagnosed HIV-positive patients during 2008-2015, 50% were linked to care, 31% started ART, and 19% were retained on ART by the time of database closure. Most patients (90-92%) at all cascade steps were adults (≥ 15 years old), among whom the majority (60-61%) were female. During 2008-2015, outcomes varied significantly across 42 administrative districts (arrondissements) of residence; cumulative linkage-to-care ranged from 23% to 69%, cumulative ART initiation among care enrollees ranged from 2% to 80%, and cumulative ART retention among ART enrollees ranged from 30% to 88%. Compared with adults, children had lower cumulative incidence of ART initiation among care enrollees (64% versus 47%) and lower cumulative retention among ART enrollees (64% versus 50%). Cumulative linkage-to-care was low and should be prioritized for improvement. Variations in outcomes by arrondissement and between adults and children require further investigation and programmatic response. |
Rates of virological suppression and drug resistance in adult HIV-1-positive patients attending primary healthcare facilities in KwaZulu-Natal, South Africa
Hunt GM , Dokubo EK , Takuva S , de Oliveira T , Ledwaba J , Dube N , Moodley P , Sabatier J , Deyde V , Morris L , Raizes E . J Antimicrob Chemother 2017 72 (11) 3141-3148 Background: KwaZulu-Natal (KZN) Province in South Africa has the highest HIV disease burden in the country, with an estimated population prevalence of 24.7%. A pilot sentinel surveillance project was undertaken in KZN to classify the proportion of adult patients failing first-line ART and to describe the patterns of drug resistance mutations (DRMs) in patients with virological failure (VF). Methods: Cross-sectional surveillance of acquired HIV drug resistance was conducted in 15 sentinel ART clinics between August and November 2013. Two population groups were surveyed: on ART for 12-15 months (Cohort A) or 24-36 months (Cohort B). Plasma specimens with viral load ≥1000 copies/mL were defined as VF and genotyped for DRMs. Results: A total of 1299 adults were included in the analysis. The prevalence of VF was 4.0% (95% CI 1.8-8.8) among 540 adults in Cohort A and 7.7% (95% CI 4.4-13.0) of 759 adults in Cohort B. Treatment with efavirenz was more likely to suppress viral load in Cohort A ( P = 0.005). Independent predictors of VF for Cohort B included male gender, advanced WHO stage at ART initiation and treatment with stavudine or zidovudine compared with tenofovir. DRMs were detected in 89% of 123 specimens with VF, including M184I/V, K103N/S, K65N/R, V106A/M and Y181C. Conclusions: VF in adults in KZN was <8% up to 3 years post-ART initiation but was associated with a high frequency of DRMs. These data identify key groups for intensified adherence counselling and highlight the need to optimize first-line regimens to maintain viral suppression. |
Trends in prevalence of advanced HIV disease at antiretroviral therapy enrollment - 10 countries, 2004-2015
Auld AF , Shiraishi RW , Oboho I , Ross C , Bateganya M , Pelletier V , Dee J , Francois K , Duval N , Antoine M , Delcher C , Desforges G , Griswold M , Domercant JW , Joseph N , Deyde V , Desir Y , Van Onacker JD , Robin E , Chun H , Zulu I , Pathmanathan I , Dokubo EK , Lloyd S , Pati R , Kaplan J , Raizes E , Spira T , Mitruka K , Couto A , Gudo ES , Mbofana F , Briggs M , Alfredo C , Xavier C , Vergara A , Hamunime N , Agolory S , Mutandi G , Shoopala NN , Sawadogo S , Baughman AL , Bashorun A , Dalhatu I , Swaminathan M , Onotu D , Odafe S , Abiri OO , Debem HH , Tomlinson H , Okello V , Preko P , Ao T , Ryan C , Bicego G , Ehrenkranz P , Kamiru H , Nuwagaba-Biribonwoha H , Kwesigabo G , Ramadhani AA , Ng'wangu K , Swai P , Mfaume M , Gongo R , Carpenter D , Mastro TD , Hamilton C , Denison J , Wabwire-Mangen F , Koole O , Torpey K , Williams SG , Colebunders R , Kalamya JN , Namale A , Adler MR , Mugisa B , Gupta S , Tsui S , van Praag E , Nguyen DB , Lyss S , Le Y , Abdul-Quader AS , Do NT , Mulenga M , Hachizovu S , Mugurungi O , Barr BAT , Gonese E , Mutasa-Apollo T , Balachandra S , Behel S , Bingham T , Mackellar D , Lowrance D , Ellerbrock TV . MMWR Morb Mortal Wkly Rep 2017 66 (21) 558-563 Monitoring prevalence of advanced human immunodeficiency virus (HIV) disease (i.e., CD4+ T-cell count <200 cells/muL) among persons starting antiretroviral therapy (ART) is important to understand ART program outcomes, inform HIV prevention strategy, and forecast need for adjunctive therapies.*,dagger, section sign To assess trends in prevalence of advanced disease at ART initiation in 10 high-burden countries during 2004-2015, records of 694,138 ART enrollees aged ≥15 years from 797 ART facilities were analyzed. Availability of national electronic medical record systems allowed up-to-date evaluation of trends in Haiti (2004-2015), Mozambique (2004-2014), and Namibia (2004-2012), where prevalence of advanced disease at ART initiation declined from 75% to 34% (p<0.001), 73% to 37% (p<0.001), and 80% to 41% (p<0.001), respectively. Significant declines in prevalence of advanced disease during 2004-2011 were observed in Nigeria, Swaziland, Uganda, Vietnam, and Zimbabwe. The encouraging declines in prevalence of advanced disease at ART enrollment are likely due to scale-up of testing and treatment services and ART-eligibility guidelines encouraging earlier ART initiation. However, in 2015, approximately a third of new ART patients still initiated ART with advanced HIV disease. To reduce prevalence of advanced disease at ART initiation, adoption of World Health Organization (WHO)-recommended "treat-all" guidelines and strategies to facilitate earlier HIV testing and treatment are needed to reduce HIV-related mortality and HIV incidence. |
Epidemiology of epidemic ebola virus disease in Conakry and surrounding prefectures, Guinea, 2014-2015
Rico A , Brody D , Coronado F , Rondy M , Fiebig L , Carcelen A , Deyde VM , Mesfin S , Retzer KD , Bilivogui P , Keita S , Dahl BA . Emerg Infect Dis 2016 22 (2) 178-83 In 2014, Ebola virus disease (EVD) in West Africa was first reported during March in 3 southeastern prefectures in Guinea; from there, the disease rapidly spread across West Africa. We describe the epidemiology of EVD cases reported in Guinea's capital, Conakry, and 4 surrounding prefectures (Coyah, Dubreka, Forecariah, and Kindia), encompassing a full year of the epidemic. A total of 1,355 EVD cases, representing approximately 40% of cases reported in Guinea, originated from these areas. Overall, Forecariah had the highest cumulative incidence (4x higher than that in Conakry). Case-fatality percentage ranged from 40% in Conakry to 60% in Kindia. Cumulative incidence was slightly higher among male than female residents, although incidences by prefecture and commune differed by sex. Over the course of the year, Conakry and neighboring prefectures became the EVD epicenter in Guinea. |
Scale-up of HIV viral load monitoring - seven Sub-Saharan African countries
Lecher S , Ellenberger D , Kim AA , Fonjungo PN , Agolory S , Borget MY , Broyles L , Carmona S , Chipungu G , De Cock KM , Deyde V , Downer M , Gupta S , Kaplan JE , Kiyaga C , Knight N , MacLeod W , Makumbi B , Muttai H , Mwangi C , Mwangi JW , Mwasekaga M , Ng'Ang ALw , Pillay Y , Sarr A , Sawadogo S , Singer D , Stevens W , Toure CA , Nkengasong J . MMWR Morb Mortal Wkly Rep 2015 64 (46) 1287-90 To achieve global targets for universal treatment set forth by the Joint United Nations Programme on human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) (UNAIDS), viral load monitoring for HIV-infected persons receiving antiretroviral therapy (ART) must become the standard of care in low- and middle-income countries (LMIC) (1). CDC and other U.S. government agencies, as part of the President's Emergency Plan for AIDS Relief, are supporting multiple countries in sub-Saharan Africa to change from the use of CD4 cell counts for monitoring of clinical response to ART to the use of viral load monitoring, which is the standard of care in developed countries. Viral load monitoring is the preferred method for immunologic monitoring because it enables earlier and more accurate detection of treatment failure before immunologic decline. This report highlights the initial successes and challenges of viral load monitoring in seven countries that have chosen to scale up viral load testing as a national monitoring strategy for patients on ART in response to World Health Organization (WHO) recommendations. Countries initiating viral load scale-up in 2014 observed increases in coverage after scale-up, and countries initiating in 2015 are anticipating similar trends. However, in six of the seven countries, viral load testing coverage in 2015 remained below target levels. Inefficient specimen transport, need for training, delays in procurement and distribution, and limited financial resources to support scale-up hindered progress. Country commitment and effective partnerships are essential to address the financial, operational, technical, and policy challenges of the rising demand for viral load monitoring. |
Strengthening HIV surveillance in the antiretroviral therapy era: rationale and design of a longitudinal study to monitor HIV prevalence and incidence in the uMgungundlovu district, KwaZulu-Natal, South Africa
Kharsany AB , Cawood C , Khanyile D , Grobler A , McKinnon LR , Samsunder N , Frohlich JA , Abdool Karim Q , Puren A , Welte A , George G , Govender K , Toledo C , Chipeta Z , Zembe L , Glenshaw MT , Madurai L , Deyde V M , Bere A . BMC Public Health 2015 15 (1) 1149 BACKGROUND: South Africa has over 6,000,000 HIV infected individuals and the province of KwaZulu-Natal (KZN) is the most severely affected. As public health initiatives to better control the HIV epidemic are implemented, timely, detailed and robust surveillance data are needed to monitor, evaluate and inform the programmatic interventions and policies over time. We describe the rationale and design of the HIV Incidence Provincial Surveillance System (HIPSS) to monitor HIV prevalence and incidence. METHODS/DESIGN: The household-based survey will include a sample of men and women from two sub-districts of the uMgungundlovu municipality (Vulindlela and the Greater Edendale) of KZN, South Africa. The study is designed as two sequential cross-sectional surveys of 10,000 randomly selected individuals aged 15-49 years to be conducted one year apart. From the cross sectional surveys, two sequential cohorts of HIV negative individuals aged 15-35 years will be followed-up one year later to measure the primary outcome of HIV incidence. Secondary outcomes include the laboratory measurements for pulmonary tuberculosis, sexually transmitted infections and evaluating tests for estimating population-level HIV incidence. Antiretroviral therapy (ART) access, HIV-1 RNA viral load, and CD4 cell counts in HIV positive individuals will assess the effectiveness of the HIV treatment cascade. Household and individual-level socio-demographic characteristics, exposure to HIV programmatic interventions and risk behaviours will be assessed as predictors of HIV incidence. The incidence rate ratio of the two cohorts will be calculated to quantify the change in HIV incidence between consecutive samples. In anticipation of better availability of population-level HIV prevention and treatment programmes leading to decreases in HIV incidence, the sample size provides 84 % power to detect a reduction of 30 % in the HIV incidence rate between surveys. DISCUSSION: The results from HIPSS will provide critical data regarding HIV prevalence and incidence in this community and will establish whether HIV prevention and treatment efforts in a "real world", non-trial setting have an impact on HIV incidence at a population level. Importantly, the study design and methods will inform future methods for HIV surveillance. |
Evaluation of nine HIV rapid test kits to develop a national HIV testing algorithm in Nigeria
Bassey O , Bond K , Adedeji A , Oke O , Abubakar A , Yakubu K , Jelpe T , Akintunde E , Ikani P , Ogundiran A , Onoja A , Kawu I , Ikwulono G , Saliu I , Nwanyawu O , Deyde V . Afr J Lab Med 2015 4 (1) BACKGROUND: Non-cold chain-dependent HIV rapid testing has been adopted in many resource-constrained nations as a strategy for reaching out to populations. HIV rapid test kits (RTKs) have the advantage of ease of use, low operational cost and short turnaround times. Before 2005, different RTKs had been used in Nigeria without formal evaluation. Between 2005 and 2007, a study was conducted to formally evaluate a number of RTKs and construct HIV testing algorithms. OBJECTIVES: The objectives of this study were to assess and select HIV RTKs and develop national testing algorithms. METHOD: Nine RTKs were evaluated using 528 well-characterised plasma samples. These comprised 198 HIV-positive specimens (37.5%) and 330 HIV-negative specimens (62.5%), collected nationally. Sensitivity and specificity were calculated with 95% confidence intervals for all nine RTKs singly and for serial and parallel combinations of six RTKs; and relative costs were estimated. RESULTS: Six of the nine RTKs met the selection criteria, including minimum sensitivity and specificity (both > 99.0%) requirements. There were no significant differences in sensitivities or specificities of RTKs in the serial and parallel algorithms, but the cost of RTKs in parallel algorithms was twice that in serial algorithms. Consequently, three serial algorithms, comprising four test kits (BundiTM, DetermineTM, Stat-Pak and Uni-GoldTM) with 100.0% sensitivity and 99.1% - 100.0% specificity, were recommended and adopted as national interim testing algorithms in 2007. CONCLUSION: This evaluation provides the first evidence for reliable combinations of RTKs for HIV testing in Nigeria. However, these RTKs need further evaluation in the field (Phase II) to re-validate their performance. |
Microevolution of highly pathogenic avian influenza A(H5N1) viruses isolated from humans, Egypt, 2007-2011
Younan M , Poh MK , Elassal E , Davis T , Rivailler P , Balish AL , Simpson N , Jones J , Deyde V , Loughlin R , Perry I , Gubareva L , Elbadry MA , Truelove S , Gaynor AM , Mohareb E , Amin M , Cornelius C , Pimentel G , Earhart K , Naguib A , Abdelghani AS , Refaey S , Klimov AI , Donis RO , Kandeel A . Emerg Infect Dis 2013 19 (1) 43-50 We analyzed highly pathogenic avian influenza A(H5N1) viruses isolated from humans infected in Egypt during 2007-2011. All analyzed viruses evolved from the lineage of subtype H5N1 viruses introduced into Egypt in 2006; we found minimal evidence of reassortment and no exotic introductions. The hemagglutinin genes of the viruses from 2011 formed a monophyletic group within clade 2.2.1 that also included human viruses from 2009 and 2010 and contemporary viruses from poultry; this finding is consistent with zoonotic transmission. Although molecular markers suggestive of decreased susceptibility to antiviral drugs were detected sporadically in the neuraminidase and matrix 2 proteins, functional neuraminidase inhibition assays did not identify resistant viruses. No other mutations suggesting a change in the threat to public health were detected in the viral proteomes. However, a comparison of representative subtype H5N1 viruses from 2011 with older subtype H5N1 viruses from Egypt revealed substantial antigenic drift. |
Monitoring seasonal influenza A evolution: rapid 2009 pandemic H1N1 surveillance with an reverse transcription-polymerase chain reaction/electro-spray ionization mass spectrometry assay
Jeng K , Massire C , Zembower TR , Deyde VM , Gubareva LV , Hsieh YH , Rothman RE , Sampath R , Penugonda S , Metzgar D , Blyn LB , Hardick J , Gaydos CA . J Clin Virol 2012 54 (4) 332-6 ![]() BACKGROUND: The emergence of the pandemic H1N1 influenza strain in 2009 reinforced the need for improved influenza surveillance efforts. A previously described influenza typing assay that utilizes RT-PCR coupled to electro-spray ionization mass spectrometry (ESI-MS) played an early role in the discovery of the pandemic H1N1 influenza strain, and has potential application for monitoring viral genetic diversity in ongoing influenza surveillance efforts. OBJECTIVES: To determine the analytical sensitivity of RT-PCR/ESI-MS influenza typing assay for identifying the pandemic H1N1 strain and describe its ability to assess viral genetic diversity. STUDY DESIGN: Two sets of pandemic H1N1 samples, 190 collected between April and June of 2009, and 69 collected between October 2009 and January 2010, were processed by the RT-PCR/ESI-MS influenza typing assay, and the spectral results were compared to reference laboratory results and historical sequencing data from the Nucleotide Database of the National Center for Biotechnology Information (NCBI). RESULTS: Strain typing concordance with reference standard testing was 100% in both sample sets, and the assay demonstrated a significant increase in influenza genetic diversity, from 10.5% non-wildtype genotypes in early samples to 69.9% in late samples (P<0.001). An NCBI search demonstrated a similar increase, from 13.4% to 45.2% (P<0.001). CONCLUSIONS: This comparison of early versus late influenza samples analyzed by RT-PCR/ESI-MS demonstrates the influenza typing assay's ability as a universal influenza detection platform to provide high-fidelity pH1N1 strain identification over time, despite increasing genetic diversity in the circulating virus. The genotyping data can also be leveraged for high-throughput influenza surveillance. |
Genetic analysis and antigenic characterization of swine origin influenza viruses isolated from humans in the United States, 1990-2010.
Shu B , Garten R , Emery S , Balish A , Cooper L , Sessions W , Deyde V , Smith C , Berman L , Klimov A , Lindstrom S , Xu X . Virology 2011 422 (1) 151-60 ![]() Swine influenza viruses (SIV) have been recognized as important pathogens for pigs and occasional human infections with swine origin influenza viruses (SOIV) have been reported. Between1990 and 2010, a total of twenty seven human cases of SOIV infections have been identified in the United States. Six viruses isolated from1990 to 1995 were recognized as classical SOIV (cSOIV) A(H1N1). After 1998, twenty-one SOIV recovered from human cases were characterized as triple reassortant (tr_SOIV) inheriting genes from classical swine, avian and human influenza viruses. Of those twenty-one tr_SOIV, thirteen were of A(H1N1), one of A(H1N2), and seven of A(H3N2) subtype. SOIV characterized were antigenically and genetically closely related to the subtypes of influenza viruses circulating in pigs but distinct from contemporary influenza viruses circulating in humans. The diversity of subtypes and genetic lineages in SOIV cases highlights the importance of continued surveillance at the animal-human interface. |
Influenza A virus nucleoprotein exploits Hsp40 to inhibit PKR activation.
Sharma K , Tripathi S , Ranjan P , Kumar P , Garten R , Deyde V , Katz JM , Cox NJ , Lal RB , Sambhara S , Lal SK . PLoS One 2011 6 (6) e20215 ![]() BACKGROUND: Double-stranded RNA dependent protein kinase (PKR) is a key regulator of the anti-viral innate immune response in mammalian cells. PKR activity is regulated by a 58 kilo Dalton cellular inhibitor (P58(IPK)), which is present in inactive state as a complex with Hsp40 under normal conditions. In case of influenza A virus (IAV) infection, P58(IPK) is known to dissociate from Hsp40 and inhibit PKR activation. However the influenza virus component responsible for PKR inhibition through P58(IPK) activation was hitherto unknown. PRINCIPAL FINDINGS: Human heat shock 40 protein (Hsp40) was identified as an interacting partner of Influenza A virus nucleoprotein (IAV NP) using a yeast two-hybrid screen. This interaction was confirmed by co-immunoprecipitation studies from mammalian cells transfected with IAV NP expressing plasmid. Further, the IAV NP-Hsp40 interaction was validated in mammalian cells infected with various seasonal and pandemic strains of influenza viruses. Cellular localization studies showed that NP and Hsp40 co-localize primarily in the nucleus. During IAV infection in mammalian cells, expression of NP coincided with the dissociation of P58(IPK) from Hsp40 and decrease PKR phosphorylation. We observed that, plasmid based expression of NP in mammalian cells leads to decrease in PKR phosphorylation. Furthermore, inhibition of NP expression during influenza virus replication led to PKR activation and concomitant increase in eIF2alpha phosphorylation. Inhibition of NP expression also led to reduced IRF3 phosphorylation, enhanced IFN beta production and concomitant reduction of virus replication. Taken together our data suggest that NP is the viral factor responsible for P58(IPK) activation and subsequent inhibition of PKR-mediated host response during IAV infection. SIGNIFICANCE: Our findings demonstrate a novel role of IAV NP in inhibiting PKR-mediated anti-viral host response and help us understand P58(IPK) mediated inhibition of PKR activity during IAV infection. |
Cluster of oseltamivir-resistant 2009 pandemic influenza A (H1N1) virus infections on a hospital ward among immunocompromised patients--North Carolina, 2009
Chen LF , Dailey NJ , Rao AK , Fleischauer AT , Greenwald I , Deyde VM , Moore ZS , Anderson DJ , Duffy J , Gubareva LV , Sexton DJ , Fry AM , Srinivasan A , Wolfe CR . J Infect Dis 2011 203 (6) 838-46 BACKGROUND: Oseltamivir resistance among 2009 pandemic influenza A (H1N1) viruses (pH1N1) is rare. We investigated a cluster of oseltamivir-resistant pH1N1 infections in a hospital ward. METHODS: We reviewed patient records and infection control measures and interviewed health care personnel (HCP) and visitors. Oseltamivir-resistant pH1N1 infections were found with real-time reverse-transcription polymerase chain reaction and pyrosequencing for the H275Y neuraminidase (NA) mutation. We compared hemagglutinin (HA) sequences from clinical samples from the outbreak with those of other surveillance viruses. RESULTS: During the period 6-11 October 2009, 4 immunocompromised patients within a hematology-oncology ward exhibited symptoms of pH1N1 infection. The likely index patient became febrile 8 days after completing a course of oseltamivir; isolation was instituted 9 days after symptom onset. Three other case patients developed symptoms 1, 3, and 5 days after the index patient. Three case patients were located in adjacent rooms. HA and NA sequences from case patients were identical. Twelve HCP and 6 visitors reported influenza symptoms during the study period. No other pH1N1 isolates from the hospital or from throughout the state carried the H275Y mutation. CONCLUSIONS: Geographic proximity, temporal clustering, presence of H275Y mutation, and viral sequence homology confirmed nosocomial transmission of oseltamivir-resistant pH1N1. Diagnostic vigilance and prompt isolation may prevent nosocomial transmission of influenza. |
RT-PCR/electrospray ionization mass spectrometry approach in detection and characterization of influenza viruses.
Deyde VM , Sampath R , Gubareva LV . Expert Rev Mol Diagn 2011 11 (1) 41-52 ![]() Reverse-transcription PCR (RT-PCR) coupled with electrospray ionization mass spectrometry (ESI-MS) is a high-throughput nucleic acid-based technology that relies on the accurate measurement of the molecular weight of PCR amplicons that can be used to deduce the base counts (number of As, Gs, Cs and Ts) of DNA. These amplicons represent highly variable regions with information-rich sequences, which are flanked by broad-range primers designed based on highly conserved loci. This technology was first introduced in 2005 for microbial identification and subtyping, and was later applied to influenza virus detection and identification. The influenza RT-PCR/ESI-MS assay allows analysis of approximately 300 samples per 24 h, and aids in the characterization of influenza viruses based on their 'core' gene signatures. Notably, this assay was used to identify one of the first cases of the 2009 H1N1 pandemic viruses. One of the main advantages of the RT-PCR/ESI-MS technology is its universality and adaptability for pathogen characterization. Efforts are being made to customize the currently used influenza surveillance assay for use in the diagnosis of the H1N1 pandemic virus. In this article, we provide a summary of known applications of the RT-PCR/ESI-MS assay in the field of influenza. |
Dual resistance to adamantanes and oseltamivir among seasonal influenza A(H1N1) viruses: 2008-2010
Sheu TG , Fry AM , Garten RJ , Deyde VM , Shwe T , Bullion L , Peebles PJ , Li Y , Klimov AI , Gubareva LV . J Infect Dis 2011 203 (1) 13-7 Two distinct genetic clades of seasonal influenza A(H1N1) viruses have cocirculated in the recent seasons: clade 2B oseltamivir-resistant and adamantane-susceptible viruses, and clade 2C viruses that are resistant to adamantanes and susceptible to oseltamivir. We tested seasonal influenza A(H1N1) viruses collected in 2008-2010 from the United States and globally for resistance to antivirals approved by the Food and Drug Administration. We report 28 viruses with both adamantane and oseltamivir (dual) resistance from 5 countries belonging to 4 distinct genotypes. Because of limited options for antiviral treatment, emergence of dual-resistant influenza viruses poses a public health concern, and their circulation needs to be closely monitored. |
Comprehensive assessment of 2009 pandemic influenza A (H1N1) virus drug susceptibility in vitro
Gubareva LV , Trujillo AA , Okomo-Adhiambo M , Mishin VP , Deyde VM , Sleeman K , Nguyen HT , Sheu TG , Garten RJ , Shaw MW , Fry AM , Klimov AI . Antivir Ther 2010 15 (8) 1151-9 ![]() BACKGROUND: Antiviral drugs are an important option for managing infections caused by influenza viruses. This study assessed the drug susceptibility of 2009 pandemic influenza A (H1N1) viruses collected globally between April 2009 and January 2010. METHODS: Virus isolates were tested for adamantane susceptibility, using pyrosequencing to detect the S31N marker of adamantane resistance in the M2 protein and biological assays to assess viral replication in cell culture. To assess neuraminidase (NA) inhibitor (NAI) susceptibility, virus isolates were tested in chemiluminescent NA inhibition assays and by pyrosequencing to detect the H275Y (H274Y in N2 numbering) marker of oseltamivir resistance in the NA. RESULTS: With the exception of three, all viruses that were tested for adamantane susceptibility (n=3,362) were resistant to this class of drugs. All viruses tested for NAI susceptibility (n=3,359) were sensitive to two US Food and Drug Administration-approved NAIs, oseltamivir (mean +/-sd 50% inhibitory concentration [IC(50)] 0.25 +/-0.12 nM) and zanamivir (mean IC(50) 0.29 +/-0.09 nM), except 23 (0.7%), which were resistant to oseltamivir, but sensitive to zanamivir. Oseltamivir-resistant viruses had the H275Y mutation in their NA and were detected in patients exposed to the drug through prophylaxis or treatment. NA activity of all viruses was inhibited by the NAIs peramivir, laninamivir (R-125489) and A-315675, except for H275Y variants, which exhibited approximately 100-fold reduction in peramivir susceptibility. CONCLUSIONS: This report provides data regarding antiviral susceptibility of 2009 pandemic influenza A (H1N1) surveillance viruses, the majority of which were resistant to adamantanes and sensitive to NAIs. These findings provide information essential for antiviral resistance monitoring and development of novel diagnostic tests for detecting influenza antiviral resistance. |
Genomic signature-based identification of influenza A viruses using RT-PCR/electro-spray ionization mass spectrometry (ESI-MS) technology
Deyde VM , Sampath R , Garten RJ , Blair PJ , Myers CA , Massire C , Matthews H , Svoboda P , Reed MS , Pohl J , Klimov AI , Gubareva LV . PLoS One 2010 5 (10) e13293 ![]() BACKGROUND: The emergence and rapid spread of the 2009 H1N1 pandemic influenza A virus (H1N1pdm) in humans highlights the importance of enhancing the capability of existing influenza surveillance systems with tools for rapid identification of emerging and re-emerging viruses. One of the new approaches is the RT-PCR electrospray ionization mass spectrometry (RT-PCR/ESI-MS) technology, which is based on analysis of base composition (BC) of RT-PCR amplicons from influenza "core" genes. Combination of the BC signatures represents a "genomic print" of an influenza A virus. METHODOLOGY/PRINCIPAL FINDINGS: Here, 757 samples collected between 2006 and 2009 were tested, including 302 seasonal H1N1, 171 H3N2, 7 swine triple reassortants, and 277 H1N1pdm viruses. Of the 277 H1N1pdm samples, 209 were clinical specimens (throat, nasal and nasopharyngeal swabs, nasal washes, blood and sputum). BC signatures for the clinical specimen from one of the first cases of the 2009 pandemic, A/California/04/2009, confirmed it as an unusual, previously unrecognized influenza A virus, with "core" genes related to viruses of avian, human and swine origins. Subsequent analysis of additional 276 H1N1pdm samples revealed that they shared the genomic print of A/California/04/2009, which differed from those of North American swine triple reassortant viruses, seasonal H1N1 and H3N2 and other viruses tested. Moreover, this assay allowed distinction between "core" genes of co-circulating groups of seasonal H1N1, such as clades 2B, 2C, and their reassortants with dual antiviral resistance to adamantanes and oseltamivir. CONCLUSIONS/SIGNIFICANCE: The RT-PCR/ESI-MS assay is a broad range influenza identification tool that can be used directly on clinical specimens for rapid and accurate detection of influenza virus genes. The assay differentiates the H1N1pdm from seasonal and other nonhuman hosts viruses. Although not a diagnostic tool, this assay demonstrates its usefulness and robustness in influenza virus surveillance and detection of novel and unusual viruses with previously unseen genomic prints. |
5'PPP-RNA induced RIG-I activation inhibits drug-resistant avian H5N1 as well as 1918 and 2009 pandemic influenza virus replication
Ranjan P , Jayashankar L , Deyde V , Zeng H , Davis WG , Pearce MB , Bowzard JB , Hoelscher MA , Jeisy-Scott V , Wiens ME , Gangappa S , Gubareva L , Garcia-Sastre A , Katz JM , Tumpey TM , Fujita T , Sambhara S . Virol J 2010 7 (1) 102 ![]() BACKGROUND: Emergence of drug-resistant strains of influenza viruses, including avian H5N1 with pandemic potential, 1918 and 2009 A/H1N1 pandemic viruses to currently used antiviral agents, neuraminidase inhibitors and M2 Ion channel blockers, underscores the importance of developing novel antiviral strategies. Activation of innate immune pathogen sensor Retinoic Acid Inducible Gene-I (RIG-I) has recently been shown to induce antiviral state. RESULTS: In the present investigation, using real time RT-PCR, immunofluorescence, immunoblot, and plaque assay we show that 5'PPP-containing single stranded RNA (5PPP-RNA), a ligand for the intracytoplasmic RNA sensor, RIG-I can be used as a prophylactic agent against known drug-resistant avian H5N1 and pandemic influenza viruses. 5'PPP-RNA treatment of human lung epithelial cells inhibited replication of drug-resistant avian H5N1 as well as 1918 and 2009 pandemic influenza viruses in a RIG-I and type 1 interferon dependant manner. Additionally, 5'PPP-RNA treatment also inhibited 2009 H1N1 viral replication in vivo in mice. CONCLUSIONS: Our findings suggest that 5PPP-RNA mediated activation of RIG-I can suppress replication of influenza viruses irrespective of their genetic make-up, pathogenicity, and drug-sensitivity status. |
In vitro antiviral activity of favipiravir (T-705) against drug-resistant influenza and 2009 A(H1N1) viruses
Sleeman K , Mishin VP , Deyde VM , Furuta Y , Klimov AI , Gubareva LV . Antimicrob Agents Chemother 2010 54 (6) 2517-24 Favipiravir (T-705) has previously been shown to have a potent antiviral effect against influenza virus and some other RNA viruses in both cell culture and in animal models. Currently, favipiravir is undergoing clinical evaluation for the treatment of influenza A and B virus infections. In this study, favipiravir was evaluated in vitro for its ability to inhibit the replication of a representative panel of seasonal influenza viruses, the 2009 A(H1N1) strains and animal viruses with pandemic potential (swine triple-reassortants, H2N2, H4N2, avian H7N2, and avian H5N1), including viruses which are resistant to the currently licensed anti-influenza drugs. All viruses were tested in a plaque reduction assay in MDCK cells, and a subset was also tested in both yield reduction and focus inhibition assays. For the majority of viruses tested, favipiravir significantly inhibited plaque formation at 3.2 muM (0.5mug/ml) (EC50s 0.19 - 22.48 muM, 0.03 - 3.53 mug/ml), and for all viruses, with the exception of a single dual resistant 2009 A(H1N1) virus, complete inhibition of plaque formation was seen at 3.2 muM (0.5mug/ml). Due to the 2009 pandemic and increased drug resistance in circulating seasonal influenza viruses, there is an urgent need for new drugs which target influenza. This study demonstrates that favipiravir inhibits in vitro replication of a wide range of influenza viruses, including those resistant to currently available drugs. |
Detection E119V and E119I mutations in influenza A (H3N2) viruses isolated from an immunocompromised patient: challenges in diagnosis of oseltamivir-resistance
Okomo-Adhiambo M , Demmler-Harrison GJ , Deyde VM , Sheu TG , Xu X , Klimov AI , Gubareva LV . Antimicrob Agents Chemother 2010 54 (5) 1834-41 ![]() The clinical use of the neuraminidase inhibitor (NAI) oseltamivir is associated with emergence of drug resistance resulting from subtype-specific neuraminidase (NA) mutations. The influenza A/Texas/12/2007 (H3N2) virus isolated from an oseltamivir-treated immunocompromised patient exhibited reduced susceptibility to oseltamivir in the chemiluminescent neuraminidase inhibition (NI) assay ( approximately 60-fold increase in IC50 compared to a control virus). When further propagated in cell culture, the isolate maintained reduced susceptibility to oseltamivir in both chemiluminescent and fluorescent NI assays ( approximately 50- and 350-fold increases in IC50, respectively). Sequencing analysis of the isolate revealed a mix of nucleotides coding for amino acids at position 119 of the NA (E119V/I). Plaque purification of the isolate yielded E119V and E119I variants, both exhibiting reduced susceptibility to oseltamivir. The E119I variant also showed decreased susceptibility to zanamivir and investigative NAIs peramivir and A-315675. The emergence of E119V variants in oseltamivir-treated patients is previously reported; however, the E119I detected here is a novel mutation which reduces susceptibility to several NAIs. Neither mutation was not detected in unpropagated original clinical specimens using either conventional sequencing or pyrosequencing, suggesting that these variants were present in very low proportions (<10%) in clinical specimens and gained dominance after virus propagation in MDCK cells. All virus isolates recovered from the patient were resistant to adamantanes. Our findings highlight the potential for emergence and persistence of multi-drug resistant influenza viruses in oseltamivir-treated immunocompromised subjects, and also highlight challenges for drug resistance diagnosis due to the genetic instability of the virus population upon propagation in cell culture. |
Detection of molecular markers of drug resistance in the 2009 pandemic influenza A (H1N1) viruses using pyrosequencing
Deyde VM , Sheu TG , Trujillo AA , Okomo-Adhiambo M , Garten R , Klimov AI , Gubareva LV . Antimicrob Agents Chemother 2009 54 (3) 1102-10 ![]() BACKGROUND: M2 blockers, amantadine and rimantadine, and neuraminidase (NA) inhibitors (NAIs), oseltamivir and zanamivir, are FDA-approved for control of influenza A virus infections. The 2009 pandemic viruses (H1N1pdm) are reassortants that acquired M and NA gene segments from a Eurasian adamantane resistant swine virus. NAI-resistance in the H1N1pdm viruses has been rare and is mainly limited to oseltamivir exposed patients. The pyrosequencing assay has been proven a useful tool in surveillance for drug resistance in seasonal influenza A viruses. METHOD: Here we provide a protocol which allows detection of adamantane resistance markers as well as the I43T change- which is unique to the H1N1pdm M2 protein. The protocol also allows detection of changes at residues V116, I117, E119, Q136, K150, D151, D199, I223, H275, and N295 in the NA, known to alter NAI drug susceptibility. RESULTS: We report here detection of the first cases of the oseltamivir resistance mutation H275Y and the change I223V in viruses from the US using the approach described in this study. Moreover, the assay permits a quick identification of the major NA group (V106/N248, I106/D248, or I106/N248) to which a pandemic virus belongs. CONCLUSIONS: pyrosequencing is well suited for detection of drug resistance markers and signature mutations in the M and NA of the pandemic H1N1 influenza viruses. |
Outbreak of antiviral drug-resistant influenza a in long-term care facility, Illinois, USA, 2008
Dharan NJ , Patton M , Siston AM , Morita J , Ramirez E , Wallis TR , Deyde V , Gubareva LV , Klimov AI , Bresee JS , Fry AM . Emerg Infect Dis 2009 15 (12) 1973-6 An outbreak of oseltamivir-resistant influenza A (H1N1) occurred in a long-term care facility. Eight (47%) of 17 and 1 (6%) of 16 residents in 2 wards had oseltamivir-resistant influenza A virus (H1N1) infections. Initial outbreak response included treatment and prophylaxis with oseltamivir. The outbreak abated, likely because of infection control measures. |
Host cell selection of influenza neuraminidase variants: implications for drug resistance monitoring in A(H1N1) viruses
Okomo-Adhiambo M , Nguyen HT , Sleeman K , Sheu TG , Deyde VM , Garten RJ , Xu X , Shaw MW , Klimov AI , Gubareva LV . Antiviral Res 2009 85 (2) 381-8 ![]() The neuraminidase inhibitors (NAIs), oseltamivir and zanamivir, are essential for treatment and prevention of influenza A and B infections. Oseltamivir resistance among influenza A (H1N1) viruses rapidly emerged and spread globally during the 2007-2008 and 2008-2009 influenza seasons. Approximately 20% and 90% of viruses tested for NAI susceptibility at CDC during these seasons, respectively, were resistant to oseltamivir (IC(50) approximately 100-3000 time>those of sensitive viruses), based on the chemiluminescent NA inhibition assay. Pyrosequencing analysis confirmed H274Y mutation (H275Y in N1 numbering) in the neuraminidase (NA) gene of oseltamivir-resistant viruses. Full NA sequence analysis of a subset of oseltamivir-resistant and sensitive virus isolates from both seasons (n=725) showed that 53 (7.3%) had mutations at residue D151 (D-->E/G/N), while 9 (1.2%) had mutations at Q136 (Q-->K) and 2 (0.3%) had mutations at both residues. Viruses with very high IC(50) for oseltamivir and peramivir, and elevated IC(50) for zanamivir, had H274Y in addition to mutations at D151 and/or Q136, residues which can potentially confer NAI-resistance based on recent N1 NA crystal structure data. Mutations at D151 without H274Y, did not elevate IC(50) for any tested NAI, however, Q136K alone significantly reduced susceptibility to zanamivir (36-fold), peramivir (80-fold) and A-315675 (114-fold) but not oseltamivir. Mutations at D151 and Q136 were present only in MDCK-grown viruses but not in matching original clinical specimens (n=33) which were available for testing, suggesting that these variants were the result of cell culture selection or they were present in very low proportions. Our findings provide evidence that propagation of influenza virus outside its natural host may lead to selection of virus variants with mutations in the NA that affect sensitivity to NAIs and thus poses implications for drug resistance monitoring and diagnostics. |
Genomic events underlying the changes in adamantane resistance among influenza A(H3N2) viruses during 2006-2008
Deyde V , Garten R , Sheu T , Smith C , Myrick A , Barnes J , Xu X , Shaw M , Klimov A , Gubareva L . Influenza Other Respir Viruses 2009 3 (6) 297-314 ![]() Please cite this paper as: Deyde et al. (2009). Genomic events underlying the changes in adamantane resistance among influenza A(H3N2) viruses during 2006-2008. Influenza and Other Respiratory Viruses 3(6), 297-314.Background Adamantanes resistance in H3N2 viruses has been increasing since 2000, and in 2005-2006 reached nearly 100% in most countries, with the circulation of the N-lineage. In 2006-2007, however, a significant decrease in resistance was observed in many regions. Objectives To explore potential links between adamantane resistance and the A(H3N2) viruses that circulated between 2006 and 2008. Methods A total of 1451 Influenza A (H3N2) viruses collected globally in 2001-2008 were screened for the presence of adamantane resistance markers. A subset of 100 viruses representing the broad genetic and geographic spectrum of these viruses was selected for complete genome sequencing and phylogenetic analyses. Results Full genome sequence analysis of 2006-2007 viruses revealed co-circulation of four distinct genotypes, designated A-D. Phylogenetic analyses demonstrated reassortment between viruses from the N-lineage and other viruses that had circulated in prior seasons, including those bearing an adamantane sensitive marker. Genotype D viruses became dominant in late 2006-2007 and continued to be the main H3N2 genotype in 2007-2008. Viruses of this genotype retained all N-lineage genome segments except PB2 and NP, which were acquired through reassortment. Conclusions The decrease in adamantane resistance at that time was due to transient co-circulation of genotypes that emerged through reassortment. Our findings emphasize the importance of complete genome sequencing in understanding the complex nature of the relationship between influenza virus evolution and antiviral resistance. The recent emergence of the pandemic multi-reassortant H1N1 virus underscores the importance of whole genome sequence monitoring for rapid detection of such unusual and novel strains. |
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