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Severe acute respiratory infections (SARI) are a leading cause of hospitalizations in children, especially due to viral pathogens. We studied the prevalence of respiratory viruses among children aged5 years hospitalized with severe acute respiratory infections (SARI) in Kashmir, India.We conducted a prospective observational study in two tertiary care hospitals from October 2013 to September 2014, systematically enrolling two children aged5 years with SARI per day. We defined SARI as history of fever or measured fever (≥38°C) and cough with onset in the last 7 days requiring hospitalization for children aged 3-59 months and as physician-diagnosed acute lower respiratory infection for children aged3 months. Trained study staff screened children within 24 hours of hospitalization for SARI and collected clinical data and nasopharyngeal swabs from enrolled participants. We tested for respiratory syncytial virus (RSV) A and B, influenza viruses, rhinoviruses (HRV)/enteroviruses, adenovirus (AdV), bocavirus (BoV), human metapneumovirus (hMPV) A and B, coronaviruses (OC43, NL65, C229E), and parainfluenza viruses (PIV) 1, 2, 3 and 4 using standardized duplex real-time polymerase chain reaction.Among 4548 respiratory illness admissions screened from October 2013 to September 2014, 1026 met the SARI case definition, and 412 were enrolled (ages = 5 days to 58 months; median = 12 months). Among enrolees, 256 (62%) were positive for any virus; RSV was the most commonly detected (n = 118, 29%) followed by HRV/enteroviruses (n = 88, 21%), PIVs (n = 31, 8%), influenza viruses (n = 18, 4%), BoV (n = 15, 4%), coronaviruses (n = 16, 4%), AdV (n = 14, 3%), and hMPV (n = 9, 2%). Fifty-four children had evidence of virus co-detection. Influenza-associated SARI was more common among children aged 1-5 years (14/18, 78%) while most RSV detections occurred in children12 months (83/118, 70%). Of the RSV viruses typed (n = 116), the majority were type B (94, 80%). Phylogenetic analysis of G gene of RSV showed circulation of the BA9 genotype with 60bp nucleotide duplication.Respiratory viruses, especially RSV, contributed to a substantial proportion of SARI hospitalizations among children5 years in north India. These data can help guide clinicians on appropriate treatment and prevention strategies.

Summary: Background: Paediatric vaccination against influenza can result in indirect protection, by reducing transmission to their unvaccinated contacts. We investigated whether influenza vaccination of children would protect them and their household members in a resource-limited setting. Methods: We did a cluster-randomised, blinded, controlled study in three villages in India. Clusters were defined as households (ie, dwellings that shared a courtyard), and children aged 6 months to 10 years were eligible for vaccination as and when they became age-eligible throughout the study. Households were randomly assigned (1:1) by a computer-based system to intramuscular trivalent inactivated influenza vaccine (IIV3) or a control of inactivated poliovirus vaccine (IPV) in the beginning of the study; vaccination occurred once a year for 3 years. The primary efficacy outcome was laboratory-confirmed influenza in a vaccinated child with febrile acute respiratory illness, analysed in the modified intention-to-treat population (ie, children who received at least one dose of vaccine, were under surveillance, and had not an influenza infection within 15 days of last vaccine dose). The secondary outcome for indirect effectiveness (surveillance study) was febrile acute respiratory illness in an unvaccinated household member of a vaccine study participant. Data from each year (year 1: November, 2009, to October, 2010; year 2: October, 2010, to October, 2011; and year 3: October, 2011, to May, 2012) were analysed separately. Safety was analysed among all participants who were vaccinated with at least one dose of the vaccine. This trial is registered with ClinicalTrials.gov, number NCT00934245. Findings: Between Nov 1, 2009, to May 1, 2012, we enrolled 3208 households, of which 1959 had vaccine-eligible children. 1010 households were assigned to IIV3 and 949 households were assigned to IPV. In 3 years, we vaccinated 4345 children (2132 with IIV3 and 2213 with IPV) from 1868 households (968 with IIV3 and 900 with IPV) with 10 813 unvaccinated household contacts. In year 1, influenza virus was detected in 151 (10%) of 1572 IIV3 recipients and 206 (13%) of 1633 of IPV recipients (total IIV3 vaccine efficacy 25·6% [95% CI 6·8–40·6]; p=0·010). In year 2, 105 (6%) of 1705 IIV3 recipients and 182 (10%) of 1814 IPV recipients had influenza (vaccine efficacy 41·0% [24·1–54·1]; p

Historical specimens collected from hospitalized children were tested for the following 13 viruses: influenza A and B; respiratory syncytial virus (RSV); parainfluenza viruses 1–3; human metapneumovirus; rhinovirus; coronaviruses 229E, OC43, NL63 and HKU1 and Adenovirus using monoplex real-time reverse transcriptase polymerase chain reaction (rRT-PCR). They were retested using TaqMan Array Card (TAC), a micro-fluidic system, capable of simultaneous multi-pathogen testing, to evaluate its sensitivity and specificity against monoplex rRT-PCR. TAC showed high sensitivity (71%–100%) and specificity (98%–100%) for these viruses in comparison to monoplex rRT-PCR. Multi-specimen detection with high sensitivity and specificity makes TAC a potentially useful tool for both surveillance and outbreak investigations.

Influenza virus non-structural protein 1 (NS1) counteracts host antiviral innate immune responses by inhibiting Retinoic acid inducible gene-I (RIG-I) activation. However, whether NS1 also specifically regulates RIG-I transcription is unknown. Here, we identify a CCAAT/Enhancer Binding Protein beta (C/EBPβ) binding site in the RIG-I promoter as a repressor element, and show that NS1 promotes C/EBPβ phosphorylation and its recruitment to the RIG-I promoter as a C/EBPβ/NS1 complex. C/EBPβ overexpression and siRNA knockdown in human lung epithelial cells resulted in suppression and activation of RIG-I expression respectively, implying a negative regulatory role of C/EBPβ. Further, C/EBPβ phosphorylation, its interaction with NS1 and occupancy at the RIG-I promoter was associated with RIG-I transcriptional inhibition. These findings provide an important insight into the molecular mechanism by which influenza NS1 commandeers RIG-I transcriptional regulation and suppresses host antiviral responses.

Background & objectives: Respiratory tract infections are common among Hajj and Umrah pilgrims which pose a public health risk of spread of respiratory infections. Influenza has been reported from Indian Hajj and Umrah returning pilgrims, but data on other respiratory pathogens are sparse in India. Here we report the presence of common respiratory viral pathogens in returning Hajj and Umrah pilgrims suffering from acute respiratory illness (ARI) in 2014-2015. Methods: Respiratory specimens (nasopharyngeal and throat swabs) were collected from 300 consenting pilgrims with ARI in the past one week and tested for influenza and Middle East Respiratory Syndrome coronavirus (MERS-CoV) and other respiratory viruses using in-house standardized quantitative real-time reverse-transcription polymerase chain reaction. Clinical features among the pathogen positive and negative patients were compared. The patients received symptomatic treatment and antivirals where appropriate and were followed telephonically to collect data on illness outcome. Results: Ninety seven (32.3%) of the 300 participants were tested positive for any virus, most common being influenza viruses (n=33, 11%). Other respiratory viruses that were detected included human coronaviruses [n=26, 8.7%; OC43 (n=19, 6.3%) and C229E (n=7, 2.3%)], rhinovirus (n=20, 6%), adenoviruses (n=8, 2.6%), parainfluenza viruses (n=7, 2.3%), respiratory syncytial virus (n=3, 1%) and bocaviruses (n=2, 0.6%). Clinical features observed in pathogen positive and pathogen negative patients did not differ significantly. Eighteen influenza positive patients were treated with oseltamivir. Interpretation & conclusions: Pilgrims returning from mass gatherings are often afflicted with respiratory pathogens with a potential to facilitate transmission of respiratory pathogens across international borders. The study reinforces the need for better infection prevention and control measures such as vaccination, health education on cough etiquette and hand hygiene.

The seasonality of influenza in the tropics complicates vaccination timing. We investigated influenza seasonality in northern India and found influenza positivity peaked in Srinagar (34.09°N) in January-March but peaked in New Delhi (28.66°N) in July-September. Srinagar should consider influenza vaccination in October-November, but New Delhi should vaccinate in May-June.

Influenza A virus (IAV), similar to other viruses, exploits the machinery of human host cells for its survival and replication. We identified α‐actinin‐4, a host cytoskeletal protein, as an interacting partner of IAV nucleoprotein (NP). We confirmed this interaction using co‐immunoprecipitation studies, first in a coupled in vitro transcription‐translation assay and then in cells either transiently co‐expressing the two proteins or infected with whole IAV. Importantly, the NP–actinin‐4 interaction was observed in several IAV subtypes, including the 2009 H1N1 pandemic virus. Moreover, immunofluorescence studies revealed that both NP and actinin‐4 co‐localized largely around the nucleus and also in the cytoplasmic region of virus‐infected A549 cells. Silencing of actinin‐4 expression resulted in not only a significant decrease in NP, M2 and NS1 viral protein expression, but also a reduction of both NP mRNA and viral RNA levels, as well as viral titers, 24 h post‐infection with IAV, suggesting that actinin‐4 was critical for viral replication. Furthermore, actinin‐4 depletion reduced the amount of NP localized in the nucleus. Treatment of infected cells with wortmannin, a known inhibitor of actinin‐4, led to a decrease in NP mRNA levels and also caused the nuclear retention of NP, further strengthening our previous observations. Taken together, the results of the present study indicate that actinin‐4, a novel interacting partner of IAV NP, plays a crucial role in viral replication and this interaction may participate in nuclear localization of NP and/or viral ribonucleoproteins. Structured digital abstract •http://www.uniprot.org/uniprot/P03466 http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0915 with http://www.uniprot.org/uniprot/O43707 by http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0006 (http://www.ebi.ac.uk/intact/interaction/EBI-9512541, http://www.ebi.ac.uk/intact/interaction/EBI-9512553)•http://www.uniprot.org/uniprot/Q8JR21 and http://www.uniprot.org/uniprot/O43707 http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0403 by http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0416 (http://www.ebi.ac.uk/intact/interaction/EBI-9514040)•http://www.uniprot.org/uniprot/Q91U50 http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0915 with http://www.uniprot.org/uniprot/O43707 by http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0006 (http://www.ebi.ac.uk/intact/interaction/EBI-9514006)•http://www.uniprot.org/uniprot/Q5L4H4 http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0407 to http://www.uniprot.org/uniprot/O43707 by http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0007 (http://www.ebi.ac.uk/intact/interaction/EBI-9512166, http://www.ebi.ac.uk/intact/interaction/EBI-9512219)•http://www.uniprot.org/uniprot/C3W6D7 http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0915 with http://www.uniprot.org/uniprot/O43707 by http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0006 (http://www.ebi.ac.uk/intact/interaction/EBI-9513951)•http://www.uniprot.org/uniprot/Q5L4H4 http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0915 with http://www.uniprot.org/uniprot/O43707 by http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0007 (http://www.ebi.ac.uk/intact/interaction/EBI-9512237)•http://www.uniprot.org/uniprot/Q6DPG0 http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0915 with http://www.uniprot.org/uniprot/O43707 by http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0006 (http://www.ebi.ac.uk/intact/interaction/EBI-9513984) •http://www.uniprot.org/uniprot/B2BU63 http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0915 with http://www.uniprot.org/uniprot/O43707 by http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0006 (http://www.ebi.ac.uk/intact/interaction/EBI-9513930) •http://www.uniprot.org/uniprot/Q5L4H4 http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0915 with http://www.uniprot.org/uniprot/O43707 by http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0018 (http://www.ebi.ac.uk/intact/interaction/EBI-9512145, http://www.ebi.ac.uk/intact/interaction/EBI-9512095) •http://www.uniprot.org/uniprot/C9S3S8 http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0915 with http://www.uniprot.org/uniprot/O43707 by http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0006 (http://www.ebi.ac.uk/intact/interaction/EBI-9513909), Human host proteins aiding the influenza A viral nucleoprotein in replication and transcription of virus and its intracellular shuttling are not well studied. The study presented here reports the dynamics of interaction between NP and actinin‐4 and the pivotal role of cytoskeletal protein in not only trafficking of NP, but also boosting its mRNA and vRNA levels, ultimately elevating viral titers.

Summary Objectives Though respiratory viruses are thought to cause substantial morbidity globally in children aged

To characterize influenza seasonality and identify the best time of the year for vaccination against influenza in tropical and subtropical countries of southern and south-eastern Asia that lie north of the equator.Weekly influenza surveillance data for 2006 to 2011 were obtained from Bangladesh, Cambodia, India, Indonesia, the Lao People's Democratic Republic, Malaysia, the Philippines, Singapore, Thailand and Viet Nam. Weekly rates of influenza activity were based on the percentage of all nasopharyngeal samples collected during the year that tested positive for influenza virus or viral nucleic acid on any given week. Monthly positivity rates were then calculated to define annual peaks of influenza activity in each country and across countries.Influenza activity peaked between June/July and October in seven countries, three of which showed a second peak in December to February. Countries closer to the equator had year-round circulation without discrete peaks. Viral types and subtypes varied from year to year but not across countries in a given year. The cumulative proportion of specimens that tested positive from June to November was60% in Bangladesh, Cambodia, India, the Lao People's Democratic Republic, the Philippines, Thailand and Viet Nam. Thus, these tropical and subtropical countries exhibited earlier influenza activity peaks than temperate climate countries north of the equator.Most southern and south-eastern Asian countries lying north of the equator should consider vaccinating against influenza from April to June; countries near the equator without a distinct peak in influenza activity can base vaccination timing on local factors.Caractériser la saisonnalité de la grippe et identifier le meilleur moment de l'année pour la vaccination contre la grippe dans les pays tropicaux et subtropicaux de l'Asie du Sud et de l'Asie du Sud-Est, qui sont situés au nord de l'équateur.Les données hebdomadaires de la surveillance de la grippe pour la période allant de 2006 à 2001 ont été obtenues auprès du Bangladesh, du Cambodge, de l'Inde, de la République démocratique populaire lao, de la Malaisie, des Philippines, de Singapour, de la Thaïlande et du Viet Nam. Les taux hebdomadaires de l'activité grippale étaient basés sur le pourcentage de tous les échantillons nasopharyngés collectés au cours de l'année et dont les tests étaient positifs au virus de la grippe ou à l'acide nucléique viral au cours d'une semaine donnée. Les pourcentages de cas positifs mensuels ont été ensuite calculés pour définir les pics annuels de l'activité grippale au sein de chaque pays et entre les pays.L'activité grippale atteint son pic entre les mois de juin/juillet et octobre dans sept pays, parmi lesquels trois pays ont présenté un second pic entre les mois de décembre et février. Les pays proches de l'équateur présentent une circulation continue sans pic distinct. Les types et sous-types viraux varient d'une année à l'autre, mais pas entre les pays au cours d'une année donnée. Le pourcentage cumulatif des prélèvements dont les tests étaient positifs de juin à novembre, était supérieur à 60% au Bangladesh, au Cambodge, en Inde, en République démocratique populaire lao, aux Philippines, en Thaïlande et au Viet Nam. Par conséquent, ces pays tropicaux et subtropicaux ont enregistré plus tôt des pics d'activité grippale que dans les pays à climat tempéré situés au nord de l'équateur.La plupart des pays de l'Asie du Sud et de l'Asie du Sud-Est, situés au nord de l'équateur, devraient envisager la vaccination contre la grippe pendant la période allant d'avril à juin. Les pays proches de l'équateur sans pic distinct d'activité grippale peuvent baser leur calendrier de vaccination sur leurs facteurs locaux.Describir la estacionalidad de la gripe e identificar el mejor momento del año para llevar a cabo la vacunación contra la gripe en países tropicales y subtropicales del sur y sureste de Asia situados al norte del ecuador.Se obtuvieron los datos semanales de vigilancia de la gripe de los años 2006 a 2011 de Bangladesh, Camboya, India, Indonesia, la República Democrática Popular Lao, Malasia, Filipinas, Singapur, Tailandia y Viet Nam. Las tasas semanales de la actividad de la gripe se basaron en el porcentaje de todas las muestras nasofaríngeas recogidas durante el año que dieron positivo en la prueba del virus de la gripe o del ácido nucleido viral en cualquier semana. Los índices de resultados positivos mensuales se calcularon luego a fin de determinar los picos anuales de la actividad de la gripe en cada uno de los países y entre países.La actividad de la gripe experimentó un aumento entre junio y julio, y octubre en siete países, tres de los cuales mostraron un segundo pico de actividad de diciembre a febrero. Los países más cercanos al ecuador presentaron una circulación durante todo el año sin picos discontinuos. Los tipos y subtipos virales variaron de año en año, pero no entre los países en un año determinado. La proporción acumulada de individuos que dieron positivo de junio a noviembre fue 60 % en Bangladesh, Camboya, India, la República Democrática Popular Lao, Filipinas, Tailandia y Viet Nam. Así, en estos países tropicales y subtropicales, los picos de actividad de la gripe se produjeron antes que en los países de clima templado al norte de la línea ecuatorial.La mayoría de los países del sur y sureste asiático situados al norte del ecuador deberían considerar llevar a cabo la vacunación contra la gripe de abril a junio; mientras que los países cercanos al ecuador sin picos marcados en la actividad de la gripe pueden basar la fecha de vacunación en factores locales.تحديد خصائص موسمية الأنفلونزا والتعرف على أفضل أوقات السنة للتطعيم ضد الأنفلونزا في البلدان المدارية ودون المدارية في جنوب وجنوب شرق آسيا الواقعة شمال خط الاستواء.تم الحصول على بيانات الترصد الأسبوعية للأنفلونزا للفترة من 2006 إلى 2011 من بنغلاديش وكمبوديا والهند وإندونيسيا وجمهورية لاو الديمقراطية الشعبية وماليزيا والفلبين وسنغافورة وتايلند وفييت نام. واستندت المعدلات الأسبوعية لنشاط الأنفلونزا على النسبة المئوية لجميع عينات البلعوم الأنفي التي تم جمعها أثناء العام والتي كانت نتائج اختباراتها إيجابية لفيروس الأنفلونزا أو الحمض النووي الفيروسي في أسبوع معين. وتم حساب معدلات الإيجابية الشهرية لتحديد فترات ذروة نشاط الأنفلونزا السنوية في كل بلد وعبر البلدان.بلغ نشاط الأنفلونزا ذروته في الفترة بين حزيران/يونيو / تموز/يوليو وتشرين الأول/أكتوبر في سبعة بلدان، حيث أظهرت ثلاثة منها ذروة ثانية في الفترة من كانون الأول/ديسمبر إلى شباط/فبراير. وشهدت البلدان الأقرب إلى خط الاستواء دوراناً طوال العام دون فترات ذروة منفصلة. واختلفت الأنماط والأنماط الفرعية للفيروس من سنة إلى أخرى، ولكن لم تختلف عبر البلدان في سنة معينة. وكانت النسبة التراكمية للعينات التي كانت نتائج اختباراتها إيجابية من حزيران/يونيو إلى تشرين الثاني/نوفمبر أكبر من 60 % في بنغلاديش وكمبوديا والهند وجمهورية لاو الديمقراطية الشعبية والفلبين وتايلند وفييت نام. ومن ثم، أظهرت هذه البلدان المدارية ودون المدارية فترات ذروة مبكرة لنشاط الأنفلونزا عن البلدان معتدلة المناخ الواقعة شمال خط الاستواء.ينبغي أن تنظر معظم بلدان جنوب وجنوب شرق آسيا الواقعة شمال خط الاستواء في التطعيم ضد الأنفلونزا في الفترة من نيسان/إبريل إلى حزيران/يونيو؛ في حين تستطيع البلدان القريبة من خط الاستواء التي لا تشهد ذروة منفصلة في نشاط الأنفلونزا تحديد توقيت التطعيم على أساس العوامل المحلية.表征赤道以北的南亚和东南亚热带和亚热带国家流感季节性特点并确定流感疫苗接种最佳时间。从孟加拉国、柬埔寨、印度、印度尼西亚、老挝、马来西亚、菲律宾、新加坡、泰国和越南收集2006年至2011年的每周流感监测数据。每周流感活动率基于的是任何给定周测试流感病毒或病毒核酸阳性的一年中收集的鼻咽样本的百分比。然后,计算每月阳性率来定义每个国家和各国之间年流感活动的峰值。七个国家中,6月/7月和10月之间出现流感活动峰值,其中三个国家在12月至2月出现第二次峰值。靠近赤道的国家长年流感传播,没有不连续的峰值。病毒类型和子类型因年份而异,但在给定年份的各个国家之间没有变化。孟加拉国、柬埔寨、印度、老挝人民民主共和国、菲律宾、泰国和越南6月至11月测试阳性的样本的累积比例 60%。因此,较之赤道以北温带气候国家,这些热带和亚热带国家出现流感活动峰值更早。赤道以北的大多数亚洲南部和东南部国家应考虑从4月到6月接种流感疫苗,赤道附近没有出现明显的流感活动峰值的国家可以根据当地因素确定疫苗接种时间。Охарактеризовать сезонность гриппа и определить лучшее время года для проведения вакцинации против гриппа в тропических и субтропических странах Южной и Юго-Восточной Азии, расположенных к северу от экватора.Еженедельные данные эпиднадзора по гриппу с 2006 по 2011 гг. были получены из Бангладеш, Камбоджи, Индии, Индонезии, Лаосской Народно-Демократической Республики, Малайзии, Филиппин, Сингапура, Таиланда и Вьетнама. Недельные показатели активности гриппа вычислялись на основе процента от общего количества всех мазков из носоглотки, собранных в течение года, показавших положительный результат на вирус гриппа или вирусную нуклеиновую кислоту в течение любой данной недели. Затем были рассчитаны месячные показатели позитивности с целью определить ежегодные пики активности гриппа в каждой из стран и во всех странах региона.Активность гриппа достигала своего пика между июнем/июлем и октябрем в семи странах, в трех из которых отмечен второй пик с декабря по февраль. Страны ближе к экватору имели круглогодичную циркуляцию заболевания без отдельных пиков. Вирусные типы и подтипы менялись из года в год, но не во всех странах в отдельно взятом году. Совокупная доля положительных образцов с июня по ноябрь составила60% в Бангладеш, Камбодже, Индии, Лаосской Народно-Демократической Республики, Филиппинах, Таиланде и Вьетнаме. Таким образом, эти тропические и субтропические страны показали более ранние пики активности гриппа по сравнению со странами с умеренным климатом к северу от экватора.Большинству стран Южной и Юго-Восточной Азии, расположенных к северу от экватора, следует рассмотреть проведение вакцинации против гриппа в сроки с апреля по июнь; страны вблизи экватора без четко выраженного пика активности гриппа могут определять сроки вакцинации исходя из местных факторов.

Background The increasing reports of Middle East Respiratory Syndrome (MERS) caused by MERS coronavirus (MERS-CoV) from many countries emphasize its importance for international travel. Muslim pilgrimages of Hajj and Umrah involve mass gatherings of international travellers. We set out to assess the presence of influenza and MERS-CoV in Hajj/Umrah returnees with acute respiratory infection. . Methods Disembarking passengers (n = 8753) from Saudi Arabia (October 2014 to April 2015) were interviewed for the presence of respiratory symptoms; 977 (11%) reported symptoms and 300 (age 26–90, median 60 years; 140 male) consented to participate in the study. After recording clinical and demographic data, twin swabs (nasopharyngeal and throat) were collected from each participant, pooled in viral transport media and tested by real-time RT PCR for MERS-CoV and influenza A and B viruses and their subtypes. Results The participants had symptoms of 1–15 days (median 5d); cough (90%) and nasal discharge (86%) being the commonest. None of the 300 participants tested positive for MERS-CoV; however, 33 (11%) tested positive for influenza viruses (A/H3N2 = 13, A/H1N1pdm09 = 9 and B/Yamagata = 11). Eighteen patients received oseltamivir. No hospitalizations were needed and all had uneventful recovery. Conclusion Despite a high prevalence of acute respiratory symptoms, MERS coV was not seen in returning pilgrims from Hajj and Umrah. However detection of flu emphasises preventive strategies like vaccination.

A unique feature of influenza A virus (IAV) life cycle is replication of the viral genome in the host cell nucleus. The nuclear import of IAV genome is an indispensable step in establishing virus infection. IAV nucleoprotein (NP) is known to mediate the nuclear import of viral genome via its nuclear localization signals. Here, we demonstrate that cellular heat shock protein 40 (Hsp40/DnaJB1) facilitates the nuclear import of incoming IAV viral ribonucleoproteins (vRNPs) and is important for efficient IAV replication. Hsp40 was found to interact with NP component of IAV RNPs during early stages of infection. This interaction is mediated by the J domain of Hsp40 and N-terminal region of NP. Drug or RNAi mediated inhibition of Hsp40 resulted in reduced nuclear import of IAV RNPs, diminished viral polymerase function and attenuates overall viral replication. Hsp40 was also found to be required for efficient association between NP and importin alpha, which is crucial for IAV RNP nuclear translocation. These studies demonstrate an important role for cellular chaperone Hsp40/DnaJB1 in influenza A virus life cycle by assisting nuclear trafficking of viral ribonucleoproteins.

Population-based active surveillance in India showed higher incidence rates for influenza A(H1N1)pdm09 among children during pandemic versus postpandemic periods (345 vs. 199/1,000 person-years), whereas adults had higher rates during postpandemic versus pandemic periods (131 vs. 69/1,000 person-years). Demographic shifts as pandemics evolve should be considered in public health response planning.

Please cite this paper as: Bali NK et al. (2012) Knowledge, attitude, and practices about the seasonal influenza vaccination among healthcare workers in Srinagar, India. Influenza and Other Respiratory Viruses 7(4), 540–545. Background Healthcare workers (HCWs) universally have a poor uptake of influenza vaccination. However, no data are available from India. Objective To explore knowledge, attitudes, and practices associated with influenza vaccination in HCWs in a temperate climate area in northern India. Patients and Methods A self-administered questionnaire was offered to all HCWs in three major hospitals of Srinagar and information sought on motivations, perceptions, preferences and practices regarding influenza vaccination. Results Of the 1750 questionnaires received, 1421 (81%) were returned. Only 62 (4·4%) HCWs had ever received influenza vaccination even as 1348 (95%) believed that influenza poses adverse potential consequences for themselves or their contacts; 1144 (81%) were aware of a vaccine against influenza and 830 (58%) of its local availability. Reasons cited by 1359 participants for not being vaccinated included ignorance about vaccine availability (435; 32%), skepticism about efficacy (248; 18%), busy schedule (166; 12%), fear of side effects (70; 4%), and a perception of not being-at-risk (82; 6%). Sixty-one percent (865) believed that vaccine programs are motivated by profit. Eighty-eight percent opined for mandatory vaccination for HCWs caring for the high-risk patients, as a part of ‘employee health program’. Most of the participants intended to get vaccinated in the current year even as 684 (48%) held that vaccines could cause unknown illness and 444 (31%) believed their adverse effects to be underreported. Conclusion Influenza vaccination coverage among HCWs is dismally low in Srinagar; poor knowledge of vaccine availability and misperceptions about vaccine effectiveness, fear of adverse effects and obliviousness to being-at-risk being important barriers. Multifaceted, adaptable measures need to be invoked urgently to increase the coverage.

Objective: Clinical case definitions used for influenza surveillance among hospitalized patients vary and need systematic evaluation. Design, setting and sample: During July 2009–August 2011, we collected clinical data and specimens (nasal and throat swabs) from rural patients hospitalized for acute medical illnesses. Specimens were tested by rRT-PCR for influenza viruses. Main outcome measures: Case definitions evaluated the following: influenza-like illness (ILI: measured fever plus cough or sore throat); severe acute respiratory illness (SARI: ILI with difficulty breathing in ≥5 years, Integrated Management of Childhood Illness–defined pneumonia or severe pneumonia, or physician diagnosed lower respiratory infection in

The influenza virus neuraminidase (NA) protein primarily aids in the release of progeny virions from infected cells. Here, we demonstrate a novel role for NA in enhancing host cell survival by activating the Src/Akt signaling axis via an interaction with carcinoembryonic antigen-related cell adhesion molecule 6/cluster of differentiation 66c (C6). NA/C6 interaction leads to increased tyrosyl phosphorylation of Src, FAK, Akt, GSK3β, and Bcl-2, which affects cell survival, proliferation, migration, differentiation, and apoptosis. siRNA-mediated suppression of C6 resulted in a down-regulation of activated Src, FAK, and Akt, increased apoptosis, and reduced expression of viral proteins and viral titers in influenza virus-infected human lung adenocarcinoma epithelial and normal human bronchial epithelial cells. These findings indicate that influenza NA not only aids in the release of progeny virions, but also cell survival during viral replication.

Please cite this paper as: Chadha et al. (2011) Multi site Virological Influenza Surveillance in India: 2004–2008. Influenza and Other Respiratory Viruses 6(3), 196–203. Background Influenza surveillance is important to identify circulating, emerging/reemerging strains and unusual epidemiological trends. With these objectives, a multisite human influenza surveillance network was initiated in India in 2004. Methods Epidemiologic data and throat swabs for laboratory testing were collected from patients with influenza-like illness (ILI) and severe acute respiratory infections (SARI). Virus isolation was carried out in Madin–Darby canine kidney cells and strains identified by hemagglutination inhibition assay. Meteorological data were collected. Results From September 2004 to December 2008, 617 (4·43%) of 13928 cases yielded isolates: 27·8% were influenza A(H1N1), 29·8% were type A(H3N2), and 42·3% were type B. The yearly type and subtype distribution varied significantly from site to site. Peak influenza activity was observed from June to August in Delhi, Pune, and Kolkata and October to December in Chennai. Maximum influenza activity was seen during the rains in Delhi, Pune, Chennai, and Kolkata in correlation with virus isolations. Multivariate analysis of ILI cases showed chill/rigors, cough, fatigue, and ILI in family, correlated positively with isolation. Genetic analysis of Indian isolates revealed that viruses matched with vaccine strains by and large. Overlapping between circulating and vaccine component strains of consecutive years was also observed. Conclusions Seasonal influenza A(H1N1), H3N2, and type B co-circulated in all regions without any particular pattern of movement of any subtype. Year-round limited influenza activity with peaks during rains was observed. Genetic drifts and varying seasonality in different parts of the country suggest that a staggered timing of vaccination may be appropriate for India.

Please cite this paper as: Broor et al. (2011) Emergence of 2009A/H1N1 cases in a tertiary care hospital in New Delhi, India. Influenza and Other Respiratory Viruses 5(6), e552–e557. Objective To determine virologic and epidemiologic characteristics of pandemic (H1N1) 2009 at All India Institute of Medical Sciences (AIIMS) a tertiary care hospital in New Delhi, India. Methods Nasal and throat swabs from patients with febrile acute respiratory illness (FARI) from August to December 2009 (n = 1401) were tested for 2009A/H1N1 and seasonal influenza A viruses by real-time RT-PCR. Results Of 1401 samples tested, 475 (33·9%) were positive for influenza A, of these majority (412; 87%) were 2009A/H1N1, whereas the remaining 63 (13%) were seasonal influenza A (49 were A/H3 and 14 were A/H1). While co-circulation of 2009A/H1N1 and A/H3 was observed in August–September, subsequent months had exclusive pandemic influenza activity (October–December 2009). Pandemic 2009A/H1N1 emergence did not follow typical seasonal influenza seasonality in New Delhi, which normally peaks in July–August, but instead showed bimodal peaks in weeks 39 and 48 in 2009. The percent of specimens testing positive for 2009A/H1N1 influenza virus was found to be highest in >5- to 18-year age group (41·2%; OR = 2·3; CI = 1·6–3·2; P = 0·00). Conclusions Taken together, our data provide high prevalence of pandemic 2009A/H1N1 in urban New Delhi with bimodal peaks in weeks 39 and 48 and highest risk group being the children of school-going age (aged >5–18).

Human T-cell lymphotropic virus types 1 and 2 (HTLV-1 and HTLV-2, respectively) are part of the Retroviridae family and members of the Deltaretrovirus genus. However, high-risk populations, such as intravenous drug users (IDUs), in which HTLV-2 infection predominates over HTLV-1 infection, are reported to have a seroprevalence of up to 20%. IDU and sex with IDUs are the most important risk factors for HTLV-2 transmission. Peripheral blood mononuclear cells (PBMCs) are appropriate specimens for nucleic acid detection and virus isolation since HTLV-1 and HTLV-2 are cell-associated viruses. Two qualitative PCR procedures, utilizing primers in the pol or tax gene region, have been used to confirm and differentiate between HTLV-1 and HTLV-2 infections. The first uses HTLV consensus primers that allow amplification of both viruses; typing is achieved either by hybridizing the product to an HTLV-1-specific or HTLV-2-specific probe or by specific restriction digestion pattern analysis. The second approach employs type-specific primers and probes in separate amplifications. Testing for antibodies to HTLV-1 and HTLV-2 should be performed for all blood donors and any patients presenting with relevant clinical signs and symptoms. A typical algorithm for HTLV testing for diagnostic purposes is outlined in this chapter. If the initial screening immunoassay (EIA or ChLIA) is reactive, a repeat assay of the same specimen is performed in duplicate.

Please cite this paper as: Koul PA., et al. (2011) Pandemic and seasonal influenza viruses among patients with acute respiratory illness in Kashmir (India). Influenza and Other Respiratory Viruses 5(6), e521–e527. Background With the emergence of pandemic influenza A (2009A/H1N1) virus in India, we sought to determine the prevalence and clinical presentations of seasonal and pandemic influenza viruses among acute respiratory illness (ARI) patients from Srinagar, a temperate climate area in northern India, during the peak winter season. Methods Combined throat and nasal swabs, obtained from 194 (108 male) presenting with ARI from January to March 2010 (Week 53-week 10), were tested by RT-PCR for influenza A and B, including 2009A/H1N1 viruses. HA1 gene of selected 2009A/H1N1-positive samples was sequenced, and phylogenetic analysis was carried out. Results Twenty-one (10·8%, age 15–80 years, median age 40 years) patients tested positive for influenza viruses: 13 (62%) for 2009A/H1N1 virus, 6 (28·5%) for seasonal influenza A (H3N2), and 2 (9·5%) for influenza B. Twelve of the 13 patients with 2009A/H1N1 presented with febrile ARI, and eight had associated comorbidities. All of the patients recovered. Phylogenetic analysis of HA gene (n = 8) revealed that all strains from Srinagar clustered in 2009A/H1N1 clade seven along with the other 2009A/H1N1 strains from India. Amino acid substitutions in the HA protein defining clade seven (P83S, S203T, and I321V) were found in almost all isolates from Srinagar. Conclusions Both seasonal and 2009A/H1N1 viruses appear to be associated with ARI in Srinagar. The 2009A/H1N1 in Srinagar is genetically similar to globally circulating clade 7 strains, with unique signature sequences in the HA gene. Further investigations into ascertain the role of these mutations in possible alteration of the virulence and transmissibility of the virus are needed.

We estimate the contribution of influenza to hospitalizations for acute exacerbations of chronic obstructive pulmonary disease (AECOPD) in Kashmir, India. Prospective surveillance for influenza among patients hospitalized with AECOPD was conducted at a tertiary care hospital. Patients had clinical data collected and nasal/throat swabs tested for influenza viruses. Outcomes among patients with and without influenza were compared with logistic regression adjusting for age and underlying conditions. During October 2010–September 2012, 498 patients hospitalized with AECOPD were enrolled, of whom 40 (8%) had received influenza vaccine. Forty (8%) had influenza; influenza virus detection peaked in winter (January–March). Patients with influenza were more likely to die during hospitalization (adjusted OR 3·4, CI 1·0–11·4) than those without.

Background. HIV and malaria in sub-Saharan Africa are associated with poor pregnancy outcome and infant survival. We studied the association of placental malaria, infant malaria and anemia, and infant HIV status with postneonatal infant mortality (PNIM) among infants of HIV-seropositive women. Methods. During 1996–2001, infants born to 570 HIV-seropositive mothers in Kisumu, Kenya were monitored monthly for malaria (parasitemia or clinical malaria) and anemia (hemoglobin level !8 g/dL) and vital status. Results. Thirty-nine deaths occurred among 112 HIV-positive infants (420/1000 live births [LBs] [95% confidence interval {CI}, 318–522 LBs]), and 36 occurred among 458 HIV-negative infants (99/1000 LBs [95% CI, 68–130 LBs]) ( ). In multivariate Cox regression analysis among HIV-negative infants, PNIM was associated P ! .001 with infant anemia (adjusted hazard ratio [AHR], 5.03 [95% CI, 1.97–12.81]) but not with placental malaria (AHR, 1.22 [95% CI, 0.50–2.95]) or infant malaria (AHR, 0.35 [95% CI, 0.10–1.21]). Among HIV-positive infants, neither placental malaria (AHR, 0.34 [95% CI, 0.10–1.10]) nor infant malaria (AHR, 0.31 [95% CI, 0.07–1.33]) or anemia (AHR, 1.07 [95% CI, 0.32–3.61]) was significantly associated with PNIM. Conclusion. In this study population, placental malaria and infant parasitemia were not risk factors for PNIM among infants of HIV-seropositive women. The prevention of infant anemia may decrease PNIM among HIVnegative infants of HIV-seropositive women.

Background The burden estimation studies for respiratory syncytial virus (RSV) have been based on varied case definitions, including case–definitions designed for influenza surveillance systems. We used all medical admissions among children aged 0–59 months to study the effect of case definitions on estimation of RSV–associated hospitalizations rates. Methods The hospital–based daily surveillance enrolled children aged 0–59 months admitted with acute medical conditions from July 2009–December 2012, from a well–defined rural population in Ballabgarh in northern India. All study participants were examined and nasal and throat swabs taken for testing by real–time polymerase chain reaction (RT–PCR) for RSV and influenza virus. Clinical data were used to retrospectively evaluate World Health Organization (WHO) case definitions (2011) commonly used for surveillance of respiratory pathogens, ie, acute respiratory illness (WHO–ARI), severe ARI (SARI) and influenza–like illness (ILI), for determination of RSV–associated hospitalization. RSV–associated hospitalization rates adjusted for admissions at non–study hospitals were calculated. Findings Out of 505 children enrolled, 82 (16.2%) tested positive for RSV. Annual incidence rates of RSV–associated hospitalization per 1000 children were highest among infants aged 0–5 months (15.2; 95% confidence interval (CI) 8.3–26.8), followed by ages 6–23 months (5.3, 95% CI 3.2–8.7) and lowest among children 24–59 months (0.5, 95% CI 0.1–1.5). The RSV positive children were more likely to have signs of respiratory distress like wheeze, chest in–drawing, tachypnea, and crepitation compared to RSV–negative based on bivariate comparisons. Other less commonly seen signs of respiratory distress, ie, nasal flaring, grunting, accessory muscle usage were also significantly associated with being RSV positive. Compared to the estimated RSV hospitalization rate based on all medical hospitalizations, the WHO–ARI case definition captured 86% of the total incidence, while case definitions requiring fever like ILI and SARI underestimated the incidence by 50–80%. Conclusions Our study suggests that RSV is a substantial cause of hospitalization among children aged

Background Despite acute respiratory infections being a major cause of death among children in developing countries including India, there is a lack of community-based studies that document its burden and aetiology. Methods A dynamic cohort of children aged 0–10 years was established in four villages in a north Indian state of Haryana from August 2012 onwards. Trained health workers conducted weekly home visits to screen children for acute respiratory infection (ARI) defined as one of the following: cough, sore throat, nasal congestion, earache/discharge, or breathing difficulty. Nurses clinically assessed these children to grade disease severity based on standard age-specific guidelines into acute upper or lower respiratory infection (AURI or ALRI) and collected nasal/throat swabs for pathogen testing. Results Our first year results show that ARI incidence in 0–10 years of age was 5.9 (5.8–6.0) per child-year with minimal gender difference, the ALRI incidence in the under-five age group was higher among boys (0.43; 0.39–0.49) as compared to girls (0.31; 0.26–0.35) per child year. Boys had 2.4 times higher ARI-related hospitalization rate as compared to girls. Conclusion ARI impose a significant burden on the children of this cohort. This study platform aims to provide better evidence for prevention and control of pneumonia in developing countries.

Background Despite the high mortality and morbidity resulting from acute respiratory infections (ARI) globally, there are few data from low-income countries on costs of ARI to inform public health policy decisions We conducted a prospective survey to assess costs of ARI episodes in selected primary, secondary, and tertiary healthcare facilities in north India where no respiratory pathogen vaccine is routinely recommended. Methods Face-to-face interviews were conducted among a purposive sample of patients with ARI from healthcare facilities. Data were collected on out-of-pocket costs of hospitalization, medical consultations, medications, diagnostics, transportation, lodging, and missed work days. Telephone surveys were conducted two weeks after medical encounters to ask about subsequent missed work and costs incurred. Costs of prescriptions and diagnostics in public facilities were supplemented with WHO-CHOICE estimates of hospital bed costs. Missed work days were assigned cost based on the national annual per capita income (US$1,104). Non-medically attended ARI cases were identified from an ongoing community-based ARI surveillance project in Faridabad. Results During September 2012-March 2013, 1766 patients with ARI were enrolled, including 451 hospitalized patients, 1056 outpatients, and 259 non-medically attended patients. The total direct cost of an ARI episode requiring outpatient care was US$4- $6 for public and $3-$10 for private institutions based on age groups. The total direct cost of an ARI episode requiring hospitalized care was $54-$120 in public and $135-$355 in private institutions. The cost of ARI among those hospitalized was highest among persons aged > = 65 years and lowest among children aged

Background: Rapid point-of-care (POC) tests provide an economical alternative for rapid diagnosis and treatment of influenza, especially in public health emergency situations. Objectives: To test the performance of a rapid influenza diagnostic test, QuickVue (Quidel) as a POC test against a real-time polymerase chain reaction (RT-PCR) assay for detection of influenza A and B in a developing country setting. Study Design: In a prospective observational design, 600 patients with influenza-like illness (ILI) or with severe acute respiratory illness (SARI) who were referred to the Influenza Clinic of a tertiary care hospital in Srinagar, India from September 2012 to April 2013, were enrolled for diagnostic testing for influenza using QuickVue or RT-PCR. All influenza A-positive patients by RT-PCR were further subtyped using primers and probes for A/H1pdm09 and A/H3. Results: Of the 600 patients, 186 tested positive for influenza A or B by RT-PCR (90 A/H1N1pdm09, 7 A/H3 and 89 influenza B), whereas only 43 tested positive for influenza (influenza A = 22 and influenza B = 21) by QuickVue. Thus, the sensitivity of the QuickVue was only 23% (95% confidence interval, CI: 17.3-29.8) and specificity was 100% (95% CI: 99.1-100) with a positive predictive value (PPV) of 100% (95% CI 91.8-100) and a negative predictive value (NPV) of 74.3% (95% CI: 70.5-77.9) as compared to RT-PCR. Conclusions: The high specificity of QuickVue suggest that this POC test can be a useful tool for patient management or triaging during a public health crisis but a low sensitivity suggests that a negative test result need to be further tested using RT-PCR.

Mycobacterium xenopi can cause opportunistic infections, particularly in persons infected with human immunodeficiency virus type 1 (HIV-1). The primary focus of this effort was to determine if M. xenopi isolates could survive and grow in human peripheral blood macrophage (MPhi), and if these isolates could promote the replication of HIV-1 in vitro. M. xenopi bacilli survived and replicated 10-fold within 48 h in human MPhi while avirulent Mycobacterium smegmatis, did not grow within the MPhi. M. xenopi bacilli when cultured with peripheral blood mononuclear cells enhanced HIV-1 replication 30- and 50-fold with the macrophage-tropic HIV-1(Ba-L) and 50- and 75-fold with T-cell-tropic strain HIV-1(LAI) by 6 days post-infection when compared to M. smegmatis. The enhanced HIV replication was associated with increased production of TNF-alpha. Partial inhibition of HIV-1 induction was observed using a neutralizing anti-TNF-alpha monoclonal antibody, pentoxifylline, and matrix metalloproteinase (MMP) inhibitor I. Similar mechanisms of pathogenesis among mycobacterial species may help elucidate better treatment approaches in HIV co-infected persons.

As vertical transmission of HIV-1 is an ongoing problem in East Africa, we analyzed HIV-1 strains of infected mothers, from Kisumu, Kenya. We sequenced the gag and gp120 regions from peripheral blood mononuclear cells (PBMC) of 15 HIV-infected mothers attending an antenatal clinic. PCR, cloning, bootscanning, using the program Simplot, and phylogenetic analyses were conducted to assign subtypes and identify recombinants. Our analyses showed two dual infections from patients who had infections with pure subtypes and recombinants subtype D. In addition, we also noted the presence of subsubtype A1 and A2, as well as unique recombinants in this area. These results imply that the HIV epidemic in western Kenya is a dynamic one and is continually evolving. Therefore, continued monitoring of the epidemic in this region is necessary if a vaccine for the area is to be developed.

The combination of unique single nucleotide polymorphisms in the CCR5 regulatory and in the CCR2 and CCR5 coding regions, defined nine CCR5 human haplogroups (HH): HHA-HHE, HHF*1, HHF*2, HHG*1, and HHG*2. Here we examined the distribution of CCR5 HH and their association with HIV infection and disease progression in 36 HIV-seronegative and 76 HIV-seropositive whites from North America and Spain [28 rapid progressors (RP) and 48 slow progressors (SP)]. Although analyses revealed that HHE frequencies were similar between HIV-seronegative and HIV-seropositive groups (25.0% vs. 32.2%, p > 0.05), HHE frequency in RP was significantly higher than that in SP (48.2% vs. 22.9%, p = 0.002). Survival analysis also showed that HHE heterozygous and homozygous were associated with an accelerated CD4 cell count decline to less than 200 cells/microL (adjusted RH 2.44, p = 0.045; adjusted RH = 3.12, p = 0.037, respectively). These data provide further evidence that CCR5 human haplogroups influence HIV-1 disease progression in HIV-infected persons.

Background Genetic polymorphism of the Fc receptor IIa for immunoglobulin (Ig) G (Fc gamma RIIa) determines IgG subclass binding. Previous studies have shown that individuals with the IgG1/3-binding Fc gamma RIIa-Arg/Arg131 genotype are relatively protected against high-density malaria, whereas individuals with the IgG2-binding Fc gamma RIIa-His/His131 genotype are at increased risk for developing cerebral malaria. The present study was undertaken to examine the relationship between Fc gamma RIIa polymorphism and placental malaria (PM) in pregnant women of known human immunodeficiency virus (HIV)-1 status. Methods Fc gamma RIIa genotype was determined in 903 pregnant women who had participated in a study designed to assess the effect that PM has on vertical transmission of HIV-1. Fc gamma RIIa polymorphism was assessed in relation to PM. Results Among HIV-negative women, there was no difference in the distribution of the Fc gamma RIIa polymorphism by PM status. However, among HIV-positive women, the frequency of the Fc gamma RIIa-His/His131 genotype was significantly higher in women with PM than in women without PM (31% vs. 22%, respectively [P=.032]). In multivariate analysis, the adjusted odds ratio for PM in HIV-positive women with the Fc gamma RIIa-His/His131 genotype versus women in the Fc gamma RIIa-His/Arg131 reference group was 1.72 (95% confidence interval, 1.11-2.69 [P=.016]). Conclusions The present study suggests that the IgG2-binding Fc gamma RIIa-His/His131 genotype is associated with enhanced susceptibility to PM in HIV-positive women but not in HIV-negative women.

The high genetic diversity of HIV-1 continues to complicate effective vaccine development. To better understand the extent of genetic diversity, intersubtype recombinants and their relative contribution to the HIV epidemic in Kenya, we undertook a detailed molecular epidemiological investigation on HIV-1-infected women attending an antenatal clinic in Kisumu, Kenya. Analysis of gag-p24 region from 460 specimens indicated that 310 (67.4%) were A, 94 (20.4%) were D, 28 (6.1%) were C, 9 (2.0%) were A2, 8 (1.7%) were G, and 11 (2.4%) were unclassifiable. Analysis of the env -gp41 region revealed that 326 (70.9%) were A, 85 (18.5%) D, 26 (5.7%) C, 9 (2.0%) each of A2 and G, 4(0.9%) unclassifiable, and 1 (0.2%) CRF02_AG. Parallel analyses of the gag-p24 and env-gp41 regions indicated that 344 (74.8%) were concordant subtypes, while the remaining 116 (25.2%) were discordant subtypes. The most common discordant subtypes were D/A (40, 8.7%), A/D (27, 5.9%), C/A (11, 2.4%), and A/C (8, 1.7%). Further analysis of a 2.1-kb fragment spanning the gag-pol region from 38 selected specimens revealed that 19 were intersubtype recombinants and majority of them were unique recombinant forms. Distribution of concordant and discordant subtypes remained fairly stable over the 4-year period (1996-2000) studied. Comparison of amino acid sequences of gag-p24 and env-gp41 regions with the subtype A consensus sequence or Kenyan candidate vaccine antigen (HIVA) revealed minor variations in the immunodominant epitopes. These data provide further evidence of high genetic diversity, with subtype A as the predominant subtype and a high proportion of intersubtype recombinants in Kenya.

OBJECTIVE To evaluate the effect of polymorphism of the Fc gamma receptor IIa, which is associated with differential human IgG subclass binding, on perinatal HIV-1 transmission. METHODS Fc gamma RIIa genotype was tested in 448 HIV-seropositive mothers and their infants from a cohort study designed to assess the effect of placental malaria on HIV vertical transmission conducted from 1996 to 2001 in western Kenya. Fc gamma RIIa polymorphism was analyzed for associations with susceptibility to perinatal HIV infection and all-cause child mortality in HIV-positive children. RESULTS Overall, 20% of infants were perinatally infected with HIV. There was no statistically significant association between maternal genotype and perinatal HIV-1 transmission. However, frequency of the infant Fc gamma RIIa His/His131 genotype was higher in HIV-positive compared with HIV-negative infants (35% and 21%, respectively), whereas the distribution was reversed (15% and 28%, respectively) for infants with the Fc gamma RIIa Arg/Arg131 genotype. Multivariate logistic regression controlling for maternal and infant confounding factors demonstrated that the odds of perinatal HIV infection in infants with the Fc gamma RIIa His/His131 versus Fc gamma RIIa His/Arg131 genotypes were significantly higher (adjusted odds ratio, 2.22; 95% confidence interval, 1.23-4.02; P = 0.009). There was no evidence for an association between HIV-positive child all-cause mortality and Fc gamma RIIa genotype. CONCLUSIONS This study provides the first evidence that the infant Fc gamma RIIa His/His131 genotype is associated with susceptibility to perinatal HIV-1 transmission and further suggests that there is a dose-response relationship for the effect of the Fc gamma RIIa His131 gene on transmission.

To determine whether maternal placental malaria is associated with an increased risk for perinatal mother-to-child HIV transmission (MTCT), we studied HIV-positive women in western Kenya. We enrolled 512 mother-infant pairs; 128 (25.0%) women had placental malaria, and 102 (19.9%) infants acquired HIV perinatally. Log10 HIV viral load and episiotomy or perineal tear were associated with increased perinatal HIV transmission, whereas low-density placental malaria (10,000 parasites/mL) was associated with reduced risk (adjusted relative risk [ARR] 0.4). Among women dually infected with malaria and HIV, high-density placental malaria (10,000 parasites/mL) was associated with increased risk for perinatal MTCT (ARR 2.0), compared to low-density malaria. The interaction between placental malaria and MTCT appears to be variable and complex: placental malaria that is controlled at low density may cause an increase in broad-based immune responses that protect against MTCT; uncontrolled, high-density malaria may simultaneously disrupt placental architecture and generate substantial antigen stimulus to HIV replication and increase risk for MTCT.

Several human monoclonal antibodies can neutralize a range of human immunodeficiency virus type 1 (HIV-1) primary isolates but their potency and related ability to suppress generation of HIV-1 escape mutants is significantly lower than the activity of antiretroviral drugs currently in clinical use. Recently, a human Fab, X5, was identified and found to neutralize primary isolates from different clades. Further improvement of the potency and breadth of HIV-1 neutralization by this antibody could be critical for its potential use in the treatment of HIV-1-infected patients. However, increasing potency of an antibody by selection from libraries may lead to a decrease in the breadth of neutralization. In an attempt to solve this problem, we subjected a random mutagenesis library of the scFv X5 to sequential rounds of selection on non-homologous HIV-1 envelope glycoproteins (Envs) dubbed sequential antigen panning (SAP). By using SAP, we identified two scFv antibodies, m6 and m9, that were tested with a panel of 33 diverse primary HIV-1 infectious isolates in an assay based on a reporter cell-line expressing high levels of CD4, CCR5 and CXCR4. The IC(50) was less than 50 microg/ml for 21 (m6) and 19 (m9) out of 29 isolates from group M (subtypes A-C, F, G and CRF-01AE) and one isolate from group N; three isolates from group O were not significantly inhibited at 50 microg/ml. The average IC(50) values for the two antibodies were significantly (p

Human T cell lymphotropic virus type I (HTLV-I) is sexually transmitted. The purpose of this study was to determine the prevalence and risk factors for cervical shedding of HTLV-I DNA among Peruvian sex workers. HTLV tax DNA was detected in cervical specimens from 43 (68%) of 63 HTLV-I-infected sex workers and in samples obtained during 113 (52%) of 216 clinic visits between 1993 and 1997. Detection of HTLV DNA was associated with the presence of > or =30 polymorphonuclear cells (PMNs) within cervical mucus per 100x microscopic field (odds ratio [OR], 4.3, 95% confidence interval [CI], 1.8-10.1) and with the presence of cervical secretions (OR, 2.0; 95% CI 1.2-3.4). Hormonal contraceptive use (OR 1.7; 95% CI, 0.8-3.6) and concomitant cervical infection by Chlamydia trachomatis (OR, 1.5; 95% CI, 0.3-4.3) or Neisseria gonorrhoeae (OR, 1.1; 95% CI, 0.6-3.7) were not significantly associated with HTLV-I shedding. Our results suggest that cervicitis may increase cervical HTLV-I shedding and the sexual transmission of this virus.

Human immunodeficiency virus type 2 (HIV-2) is the result of cross-species transmission of simian immunodeficiency virus (SIV) from sooty mangabey monkeys to humans. Primer pairs (intHIV-2/SIV) based on a region of integrase that has considerable homology across HIV-2 and SIV lineages were designed to develop a broadly cross-reactive molecular assay to detect lentivirus infection in primates. The intHIV-2/SIV primers detect HIV-2 and simian viruses SIVcpz, SIVsmm, SIVsyk, SIVagm, and SIVmnd. The primers are also capable of amplifying some HIV-1 strains. Additionally, sequences from the integrase amplicons were of sufficient genetic diversity to permit not only phylogenetic clustering of all simian viruses to their respective lineages but also HIV type and group classification. Thus, the primers described here provide a method to detect primate lentiviruses from diverse species of nonhuman primates, as well as from persons infected with HIV-1 and HIV-2.

Background Two of the fusion inhibitors T-20 and 5-helix polypeptide have been shown to be potent inhibitors of cell-to-cell fusion and are currently under investigation as therapy for HIV-1. Objectives To examine variability of HIV-1 gp41 heptads repeat regions (HR1 and HR2), with special emphasis on the presence of T-20 resistance mutations and 5-helix variability at critical epitopes, in treatment-naive patients infected with diverse HIV-1 subtypes from different geographic regions. Methods A total of 150 specimens representing HIV-1 group M subtypes (A-G) from persons naive to HIV-1 viral entry inhibitor therapy were used to amplify and sequence a 506 bp segment of transmembrane protein. Results In general, both HR1 (a.a. 540-593) and HR2 (a.a. 628-673) domains were highly conserved. Sequence analysis of the T-20 resistant domain (a.a. 547-549, GIV) revealed that 99% of the specimens (149 of 150) carried a T-20 sensitive genotype. The critical epitopes involved in the 5-helix interaction include residues at positions 628W, 631W, 635I, 638Y, 642I, 645L, 649S, 652Q, 656N, and 659E. Analysis of the 150 specimens revealed that all had identical residues at six of these positions, whereas two positions had minor variations (635 and 649) and two (645 and 659) appeared to have subtype-specific substitutions. Conclusions This data indicates that there is limited resistance to T-20 in these worldwide populations and that the critical epitopes for effective 5-helix binding are highly conserved across all subtypes. Taken together, these data suggest that T-20 and 5-helix should provide useful additives to current antiretroviral therapy for clinical management of HIV disease.

To establish a baseline for monitoring resistance to protease inhibitors (PIs) and examining the efficacy of their use among persons in Cameroon infected with human immunodeficiency virus type 1 (HIV-1), we analyzed genetic variability and PI resistance-associated substitutions in PCR-amplified protease (PR) sequences in strains isolated from 110 HIV-1-infected, drug-naïve Cameroonians. Of the 110 strains, 85 were classified into six HIV-1 PR subtypes, A ( n = 1), B ( n = 1), F ( n = 4), G ( n = 7), H ( n = 1), and J ( n = 7), and a circulating recombinant form, CRF02-AG ( n = 64). PR genes from the remaining 25 (23%) specimens were unclassifiable, whereas 2% (7 of 301) unclassifiable PR sequences were reported for a global collection. Two major PI resistance-associated mutations, 20M and 24I, were detected in strains from only two specimens, whereas secondary mutations were found in strains from all samples except one strain of subtype B and two strains of CRF02-AG. The secondary mutations showed the typical PI resistance-associated pattern for non-subtype B viruses in both classifiable and unclassifiable PR genes, with 36I being the predominant (99%) mutation, followed by 63P (18%), 20R (15%), 77I (13%), and 10I or 10V (11%). Of these mutations, dual and triple PI resistance-associated substitutions were found in 38% of all the Cameroonian strains. Compared with classifiable PR sequences, unclassifiable sequences had significantly more dual and triple substitutions (64% versus 30%; P = 0.004). Phenotypic and clinical evaluations are needed to estimate whether PI resistance during antiretroviral drug treatment occurs more rapidly in individuals infected with HIV-1 strains harboring multiple PI resistance-associated substitutions. This information may be important for determination of appropriate drug therapies for HIV-1-infected persons in Cameroon, where more than one-third of HIV-1 strains were found to carry dual and triple minor PI resistance-associated mutations.

The global burden of influenza is increasingly recognized, but data from India remain sparse. We conducted a multi-site population-based surveillance study to estimate and compare rates of influenza-associated hospitalization at two rural Indian health and demographic surveillance system (HDSS) sites at Ballabgarh and Vadu during 2010-2012.Prospective facility-based surveillance for all hospitalizations (excluding those for trauma, elective surgery and obstetric, ophthalmic or psychiatric reasons) was conducted at 72 health facilities. After collection of clinical details, patients had nasopharyngeal swabs taken and tested by reverse transcription polymerase chain reaction for influenza viruses. Annual healthcare utilization surveys (HUS) were conducted in HDSS households to identify proportion of hospitalizations occurring at non-study facilities to adjust for hospitalizations missed through facility-based surveillance.HUS showed that 69% and 67% of hospitalizations occurred at study facilities at Ballabgarh and Vadu, respectively. Overall, 6004 patients hospitalized with acute medical illness at participating facilities were enrolled (1717 from Ballabgarh; 4287 from Vadu). The proportion of patients with influenza was higher at Vadu than Ballabgarh annually (2010: 21% vs. 5%, p 0.05; 2011: 18% vs. 5%, p 0.05; 2012: 23% vs. 5%, p 0.05). Annual adjusted influenza-associated hospitalization rates were 5-11 fold higher in Vadu (20.3-51.6 per 10,000) vs Ballabgarh (4.4-6.3 per 10,000). At both sites, influenza A/H1N1pdm09 and B predominated during 2010, A/H3N2 and B during 2011, and A/H1N1pdm09 and B during 2012.The markedly different influenza hospitalization rates by season and across communities in India highlight the need for sustained multi-site surveillance system for estimating national influenza disease burden. That would be the first step for initiating discussions around Influenza prevention and control strategies in the country.

Some parts of world, including India observed a recrudescent wave of influenza A/H1N1pdm09 in 2012. We undertook a study to examine the circulating influenza strains, their clinical association and antigenic characteristics to understand the recrudescent wave of A/H1N1pdm09 from November 26, 2012 to Feb 28, 2013 in Kashmir, India. Of the 751 patients (545 outpatient and 206 hospitalized) presenting with acute respiratory infection at a tertiary care hospital in Srinagar; 184 (24.5%) tested positive for influenza. Further type and subtype analysis revealed that 106 (58%) were influenza A (H1N1pdm09 =105, H3N2=1) and 78 (42%) were influenza B. The influenza positive cases had a higher frequency of chills, nasal discharge, sore throat, body aches and headache, compared to influenza negative cases. Of the 206 patients hospitalized for pneumonia/acute respiratory distress syndrome or an exacerbation of an underlying lung disease, 34 (16.5%) tested positive for influenza (22 for H1N1pdm09, 11 for influenza B). All influenza-positive patients received oseltamivir and while most patients responded well to antiviral therapy and supportive care, 6 patients (4 with H1N1pdm09 and 2 with influenza B) patients died of progressive respiratory failure and multi-organ dysfunction. Following a period of minimal circulation, H1N1pdm09 re-emerged in Kashmir in 2012-2013, causing serious illness and fatalities. As such the healthcare administrators and policy planners need to be wary and monitor the situation closely.

Phenotypic change and broader coreceptor usage by HIV-1 have been associated with disease progression. HIV-1 coreceptor usage by primary isolates obtained from HIV-1-infected and HIV-1/HTLV-II-coinfected individuals was determined. HIV-1 was isolated from 15 of 20 HIV-1-infected and 17 of 24 HIV-1/HTLV-II-coinfected individuals. None of the isolates from either the HIV-1-infected or the coinfected group infected CCR5delta32 PBMCs, suggesting that they all were R5-tropic. Further, both spontaneous and PHA-stimulated production of MIP-1beta and RANTES were similar in HIV-1-infected and coinfected individuals. These data indicate that coinfection with HTLV-II has no effect on HIV-1 coreceptor usage or ex vivo beta-chemokine production.