Last data update: Nov 04, 2024. (Total: 48056 publications since 2009)
Records 1-30 (of 43 Records) |
Query Trace: Bahl J[original query] |
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Factors influencing vaccine receipt during a 2018 pediatric typhoid conjugate vaccine campaign in Navi Mumbai, India
Borhade P , LeBoa C , Jayaprasad N , Date K , Haldar P , Harvey P , Shimpi R , An Q , Zhang C , Horng L , Fagerli K , Yewale VN , Daruwalla S , Dharmapalan D , Gavhane J , Joshi S , Rai R , Rathod V , Shetty K , Warrier DS , Yadav S , Chakraborty D , Bahl S , Katkar A , Kunwar A , Andrews JR , Bhatnagar P , Dutta S , Luby SP , Hoffman SA . Am J Trop Med Hyg 2024 In 2018, the Navi Mumbai Municipal Corporation implemented phase 1 of a public sector typhoid conjugate vaccine campaign in Navi Mumbai, India, targeting all children aged 9 months to 14 years within its administrative boundaries. To assess associations with receipt of vaccine in phase 1, we used generalized estimating equations to calculate estimates of vaccination by child-, household-, and community-level demographics (child education and age; household head education, income, and occupation; community informal settlement percent). Campaign vaccine receipt was most associated with children enrolled in school (odds ratio [OR] = 3.84, 95% CI: 2.18-6.77), the lowest household income tertile when divided into three equal parts (OR = 1.64, 95% CI: 1.43-1.84), and lower community-level socioeconomic status (OR = 1.06, 95% CI: 1.04-1.08 per 10% informal settlement proportion). The campaign was successful in reaching the most underserved populations of its target communities. |
Clinical and epidemiological characteristics of mpox cases identified through case-based surveillance in India, July 2022-January 2023
Kuriakose S , Gupta RK , Kumar A , Kumar J , Kulkarni S , Chauhan H , Relhan V , Meenakshy V , Gopalakrishnan LG , Singh SK , Bahl A , Tanwar S , Dikid T . Indian J Public Health 2024 68 (3) 374-379 BACKGROUND: Of the 43 mpox cases reported by the WHO in South East Asia between January 2022 and March 2023, 24 (56%) were from India. OBJECTIVES: We describe the clinical and epidemiological profile of cases identified through India's hospital case-based surveillance. MATERIALS AND METHODS: We identified mpox cases as a positive result for mpox virus polymerase-chain-reaction assay, reported through surveillance from July 1, 2022 to January 7, 2023. Cases and clinicians were interviewed, and data were abstracted from the medical records. We conducted contact tracing among family, close social networks, and healthcare personnel staff for the first 17 cases. We collected the data on sociodemographics, clinical findings, and behavior, and described data using summary statistics. RESULTS: We identified 24 laboratory-confirmed cases (42% females, median age 30 years, range 22-38), including one death (case fatality rate 4.2%). We collected clinical and behavioural data from 21 of 24 cases. All had rashes with vesicles and genital lesions; 7 (33%) reported genital lesions as the first symptom; and 3 (13%) reported complications. Among the 21 cases, all were sexually active, none self-identified as men having sex with men (MSM), and 6 (29%) reported multiple sex partners. We identified 51 contacts of the first 17 reported cases, none reported symptoms suggestive of mpox. CONCLUSION: The clinical and behavioral characteristics of mpox cases in India are consistent with the global 2022 outbreak, with the exception that no cases in India reported MSM. Most were sexually active young adult economic migrants and developed genital lesions. |
Sequence-based detection of emerging antigenically novel influenza A viruses
Forna A , Weedop KB , Damodaran L , Hassell N , Kondor R , Bahl J , Drake JM , Rohani P . Proc Biol Sci 2024 291 (2028) 20240790 The detection of evolutionary transitions in influenza A (H3N2) viruses' antigenicity is a major obstacle to effective vaccine design and development. In this study, we describe Novel Influenza Virus A Detector (NIAViD), an unsupervised machine learning tool, adept at identifying these transitions, using the HA1 sequence and associated physico-chemical properties. NIAViD performed with 88.9% (95% CI, 56.5-98.0%) and 72.7% (95% CI, 43.4-90.3%) sensitivity in training and validation, respectively, outperforming the uncalibrated null model-33.3% (95% CI, 12.1-64.6%) and does not require potentially biased, time-consuming and costly laboratory assays. The pivotal role of the Boman's index, indicative of the virus's cell surface binding potential, is underscored, enhancing the precision of detecting antigenic transitions. NIAViD's efficacy is not only in identifying influenza isolates that belong to novel antigenic clusters, but also in pinpointing potential sites driving significant antigenic changes, without the reliance on explicit modelling of haemagglutinin inhibition titres. We believe this approach holds promise to augment existing surveillance networks, offering timely insights for the development of updated, effective influenza vaccines. Consequently, NIAViD, in conjunction with other resources, could be used to support surveillance efforts and inform the development of updated influenza vaccines. |
Field effectiveness of a typhoid conjugate vaccine: The 2018 Navi Mumbai Pediatric TCV Campaign
Date K , LeBoa C , Hoffman SA , Haldar P , Harvey P , An Q , Zhang C , Yewale VN , Daruwalla S , Dharmapalan D , Gavhane J , Joshi S , Rai R , Rathod V , Shetty K , Warrier DS , Yadav S , Shimpi R , Jayaprasad N , Horng L , Fagerli K , Borhade P , Chakraborty D , Katkar A , Kunwar A , Andrews JR , Bahl S , Bhatnagar P , Dutta S , Luby SP . Am J Trop Med Hyg 2024 Typbar-TCV®, a typhoid conjugate vaccine (TCV), was prequalified by the World Health Organization in 2017. We evaluated its effectiveness in a mass vaccination program targeting children 9 months to 14 years in Navi Mumbai, India, from September 2018 to July 2020. We compared laboratory-confirmed typhoid cases from six clinical sites with age-matched community controls. Of 38 cases, three (8.6%) received TCV through the campaign, compared with 53 (37%) of 140 controls. The adjusted odds ratio of typhoid fever among vaccinated children was 0.16 (95% CI: 0.05-0.55), equivalent to a vaccine effectiveness of 83.7% (95% CI: 45.0-95.3). Vaccine effectiveness of Typbar-TCV in this large public sector vaccine introduction was similar to prior randomized controlled trials, providing reassurance to policymakers that TCV effectiveness is robust in a large-scale implementation. |
Progress toward measles and rubella elimination - Indonesia, 2013-2022
Chacko S , Kamal M , Hastuti EB , Mildya F , Kelyombar C , Voronika V , Yosephine P , Tandy G , Anisiska D , Karolina S , Dewi LA , Khanal S , Bahl S , Wijayanti F , Merrill RD , Hsu CH , Morales M . MMWR Morb Mortal Wkly Rep 2023 72 (42) 1134-1139 In 2019, Indonesia and the other countries in the World Health Organization South-East Asia Region adopted the goal of measles and rubella elimination by 2023. This report describes Indonesia's progress toward measles and rubella elimination during 2013-2022. During this period, coverage with a first dose of measles-containing vaccine (MCV) decreased from 87% to 84%, and coverage with a second MCV dose decreased from 76% to 67%. After rubella vaccine was introduced in 2017, coverage with the first dose of rubella-containing vaccine increased approximately fivefold, from 15% in 2017 to 84% in 2022. During 2013-2021, annual reported measles incidence decreased by 95%, from 33.2 to 1.4 cases per million population; reported rubella incidence decreased 89%, from 9.3 to 1.0 cases per million population. However, a large surge in measles and rubella cases occurred in 2022, with a reported measles incidence of 29 cases per million and a reported rubella incidence of 3 per million, primarily related to disruption in immunization services caused by the COVID-19 pandemic. In 2022, approximately 26 million children (an estimated 73% of the target population) received a combined measles- and rubella-containing vaccine during supplementary immunization activities completed in 32 provinces. Progress toward measles and rubella elimination in Indonesia has been made; however, continued and urgent efforts are needed to restore routine immunization services that were adversely affected by the COVID-19 pandemic and close immunity gaps to accelerate progress toward measles and rubella elimination. |
Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)
Kuhn JH , Abe J , Adkins S , Alkhovsky SV , Avšič-Županc T , Ayllón MA , Bahl J , Balkema-Buschmann A , Ballinger MJ , Kumar Baranwal V , Beer M , Bejerman N , Bergeron É , Biedenkopf N , Blair CD , Blasdell KR , Blouin AG , Bradfute SB , Briese T , Brown PA , Buchholz UJ , Buchmeier MJ , Bukreyev A , Burt F , Büttner C , Calisher CH , Cao M , Casas I , Chandran K , Charrel RN , Kumar Chaturvedi K , Chooi KM , Crane A , Dal Bó E , Carlos de la Torre J , de Souza WM , de Swart RL , Debat H , Dheilly NM , Di Paola N , Di Serio F , Dietzgen RG , Digiaro M , Drexler JF , Duprex WP , Dürrwald R , Easton AJ , Elbeaino T , Ergünay K , Feng G , Firth AE , Fooks AR , Formenty PBH , Freitas-Astúa J , Gago-Zachert S , Laura García M , García-Sastre A , Garrison AR , Gaskin TR , Gong W , Gonzalez JJ , de Bellocq J , Griffiths A , Groschup MH , Günther I , Günther S , Hammond J , Hasegawa Y , Hayashi K , Hepojoki J , Higgins CM , Hongō S , Horie M , Hughes HR , Hume AJ , Hyndman TH , Ikeda K , Jiāng D , Jonson GB , Junglen S , Klempa B , Klingström J , Kondō H , Koonin EV , Krupovic M , Kubota K , Kurath G , Laenen L , Lambert AJ , Lǐ J , Li JM , Liu R , Lukashevich IS , MacDiarmid RM , Maes P , Marklewitz M , Marshall SH , Marzano SL , McCauley JW , Mirazimi A , Mühlberger E , Nabeshima T , Naidu R , Natsuaki T , Navarro B , Navarro JA , Neriya Y , Netesov SV , Neumann G , Nowotny N , Nunes MRT , Ochoa-Corona FM , Okada T , Palacios G , Pallás V , Papa A , Paraskevopoulou S , Parrish CR , Pauvolid-Corrêa A , Pawęska JT , Pérez DR , Pfaff F , Plemper RK , Postler TS , Rabbidge LO , Radoshitzky SR , Ramos-González PL , Rehanek M , Resende RO , Reyes CA , Rodrigues TCS , Romanowski V , Rubbenstroth D , Rubino L , Runstadler JA , Sabanadzovic S , Sadiq S , Salvato MS , Sasaya T , Schwemmle M , Sharpe SR , Shi M , Shimomoto Y , Kavi Sidharthan V , Sironi M , Smither S , Song JW , Spann KM , Spengler JR , Stenglein MD , Takada A , Takeyama S , Tatara A , Tesh RB , Thornburg NJ , Tian X , Tischler ND , Tomitaka Y , Tomonaga K , Tordo N , Tu C , Turina M , Tzanetakis IE , Maria Vaira A , van den Hoogen B , Vanmechelen B , Vasilakis N , Verbeek M , von Bargen S , Wada J , Wahl V , Walker PJ , Waltzek TB , Whitfield AE , Wolf YI , Xia H , Xylogianni E , Yanagisawa H , Yano K , Ye G , Yuan Z , Zerbini FM , Zhang G , Zhang S , Zhang YZ , Zhao L , Økland AL . J Gen Virol 2023 104 (8) In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV. |
Population structure and antimicrobial resistance patterns of Salmonella Typhi and Paratyphi A amid a phased municipal vaccination campaign in Navi Mumbai, India
da Silva KE , Date K , Hirani N , LeBoa C , Jayaprasad N , Borhade P , Warren J , Shimpi R , Hoffman SA , Mikoleit M , Bhatnagar P , Cao Y , Haldar P , Harvey P , Zhang C , Daruwalla S , Dharmapalan D , Gavhane J , Joshi S , Rai R , Rathod V , Shetty K , Warrier DS , Yadav S , Chakraborty D , Bahl S , Katkar A , Kunwar A , Yewale V , Dutta S , Luby SP , Andrews JR . mBio 2023 14 (4) e0117923 We performed whole-genome sequencing of 174 Salmonella Typhi and 54 Salmonella Paratyphi A isolates collected through prospective surveillance in the context of a phased typhoid conjugate vaccine introduction in Navi Mumbai, India. We investigate the temporal and geographical patterns of emergence and spread of antimicrobial resistance. We evaluated the relationship between the spatial distance between households and genetic clustering of isolates. Most isolates were non-susceptible to fluoroquinolones, with nearly 20% containing ≥3 quinolone resistance-determining region mutations. Two H58 isolates carried an IncX3 plasmid containing bla(SHV-12), associated with ceftriaxone resistance, suggesting that the ceftriaxone-resistant isolates from India independently evolved on multiple occasions. Among S. Typhi, we identified two main clades circulating (2.2 and 4.3.1 [H58]); 2.2 isolates were closely related following a single introduction around 2007, whereas H58 isolates had been introduced multiple times to the city. Increasing geographic distance between isolates was strongly associated with genetic clustering (odds ratio [OR] = 0.72 per km; 95% credible interval [CrI]: 0.66-0.79). This effect was seen for distances up to 5 km (OR = 0.65 per km; 95% CrI: 0.59-0.73) but not seen for distances beyond 5 km (OR = 1.02 per km; 95% CrI: 0.83-1.26). There was a non-significant reduction in odds of clustering for pairs of isolates in vaccination communities compared with non-vaccination communities or mixed pairs compared with non-vaccination communities. Our findings indicate that S. Typhi was repeatedly introduced into Navi Mumbai and then spread locally, with strong evidence of spatial genetic clustering. In addition to vaccination, local interventions to improve water and sanitation will be critical to interrupt transmission. IMPORTANCE Enteric fever remains a major public health concern in many low- and middle-income countries, as antimicrobial resistance (AMR) continues to emerge. Geographical patterns of typhoidal Salmonella spread, critical to monitoring AMR and planning interventions, are poorly understood. We performed whole-genome sequencing of S. Typhi and S. Paratyphi A isolates collected in Navi Mumbai, India before and after a typhoid conjugate vaccine introduction. From timed phylogenies, we found two dominant circulating lineages of S. Typhi in Navi Mumbai-lineage 2.2, which expanded following a single introduction a decade prior, and 4.3.1 (H58), which had been introduced repeatedly from other parts of India, frequently containing "triple mutations" conferring high-level ciprofloxacin resistance. Using Bayesian hierarchical statistical models, we found that spatial distance between cases was strongly associated with genetic clustering at a fine scale (<5 km). Together, these findings suggest that antimicrobial-resistant S. Typhi frequently flows between cities and then spreads highly locally, which may inform surveillance and prevention strategies. |
Programmatic Effectiveness of a Pediatric Typhoid Conjugate Vaccine Campaign in Navi Mumbai, India (preprint)
Hoffman SA , LeBoa C , Date K , Haldar P , Harvey P , Shimpi R , An Q , Zhang C , Jayaprasad N , Horng L , Fagerli K , Borhade P , Chakraborty D , Bahl S , Katkar A , Kunwar A , Yewale V , Andrews JR , Bhatnagar P , Dutta S , Luby SP . medRxiv 2022 27 Background: The WHO recommends vaccines for prevention and control of typhoid fever, especially where antimicrobial-resistant typhoid circulates. In 2018 the Navi Mumbai Municipal Corporation (NMMC), implemented a TCV campaign. The campaign targeted all children aged 9-months through 14-years within NMMC boundaries (~320,000 children) over 2 vaccination phases. The phase 1 campaign occurred from July 14-August 25, 2018 (71% coverage, ~113,420 children). We evaluated the campaign's programmatic effectiveness in reducing typhoid cases at the community level. Method(s): We established prospective, blood culture-based surveillance at 6 hospitals in Navi Mumbai, offering blood cultures to children presenting with fever for at least 3 days. We employed a cluster-randomized test-negative design to estimate the effectiveness of the vaccination campaign on pediatric typhoid cases. We matched culture-confirmed typhoid cases with up to 3 culture-negative controls by age and date of blood culture and assessed community vaccine campaign phase as an exposure using conditional logistic regression. Result(s): Between September 1, 2018-March 31, 2021, we identified 81 typhoid cases and matched these with 238 controls. Cases were 0.44 times as likely to live in vaccine campaign communities (campaign effectiveness, 56%, 95%CI: 25%-74%, p=0.002). Cases >= 5-years-old were 0.37 times as likely (95% CI: 0.19-0.70; p-value = 0.002) and cases during the first year of surveillance were 0.30 times as likely (95% CI: 0.14-0.64; p-value = 0.002) to live in vaccine campaign communities. Conclusion(s): Our findings support the use of TCV mass vaccination campaigns as effective population-based tools to combat typhoid fever. 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-NC-ND 4.0 International license. |
Progress toward rubella elimination - World Health Organization South-East Asia Region, 2013-2021
Khanal S , Bahl S , Sangal L , Dhongde D , O'Connor PM , Crowcroft NS , Morales M . MMWR Morb Mortal Wkly Rep 2023 72 (25) 678-682 During 2013, the 11 countries of the World Health Organization (WHO) South-East Asia Region* (SEAR) adopted the goals of measles elimination and rubella and congenital rubella syndrome (CRS) control(†) by 2020. During 2019, SEAR countries declared a broader goal for eliminating both measles and rubella(§) by 2023 (1). Before 2013, only five SEAR countries had introduced rubella-containing vaccine (RCV). This report updates a previous report and describes progress toward rubella elimination in SEAR during 2013-2021 (2). During 2013-2021, six SEAR countries introduced RCV; all countries in the Region now use RCV in routine immunization. Routine immunization coverage with the first dose of a rubella-containing vaccine (RCV1) increased >600%, from 12% during 2013 to 86% during 2021, and an estimated 515 million persons were vaccinated via RCV supplementary immunization activities (SIAs)(¶) during 2013-2021. During this time, annual reported rubella incidence declined by 80%, from 5.5 to 1.1 cases per million population. Maldives and Sri Lanka are verified as having achieved rubella elimination; Bhutan, North Korea, and Timor-Leste have halted endemic transmission of rubella virus for >36 months. SEAR has made substantial progress toward rubella elimination; however, intensified measures are needed to achieve elimination. |
Delivery cost of the first public sector introduction of typhoid conjugate vaccine in Navi Mumbai, India
Song D , Pallas SW , Shimpi R , Ramaswamy N , Haldar P , Harvey P , Bhatnagar P , Katkar A , Jayaprasad N , Kunwar A , Bahl S , Morgan W , Hutubessy R , Date K , Mogasale V . PLOS Glob Public Health 2023 3 (1) e0001396 Navi Mumbai Municipal Corporation (NMMC), a local government in Mumbai, India, implemented the first public sector TCV campaign in 2018. This study estimated the delivery costs of this TCV campaign using a Microsoft Excel-based tool based on a micro-costing approach from the government (NMMC) perspective. The campaign's financial (direct expenditures) and economic costs (financial costs plus the monetized value of additional donated or existing items) incremental to the existing immunization program were collected. The data collection methods involved consultations with NMMC staff, reviews of financial and programmatic records of NMMC and the World Health Organization (WHO), and interviews with the health staff of sampled urban health posts (UHPs). Three UHPs were purposively sampled, representing the three dominant residence types in the catchment area: high-rise, slum, and mixed (high-rise and slum) areas. The high-rise area UHP had lower vaccination coverage (47%) compared with the mixed area (71%) and slum area UHPs (76%). The financial cost of vaccine and vaccination supplies (syringes, safety boxes) was $1.87 per dose, and the economic cost was $2.96 per dose in 2018 US dollars. Excluding the vaccine and vaccination supplies cost, the financial delivery cost across the 3 UHPs ranged from $0.37 to $0.53 per dose, and the economic delivery cost ranged from $1.37 to $3.98 per dose, with the highest delivery costs per dose in the high-rise areas. Across all 11 UHPs included in the campaign, the weighted average financial delivery cost was $0.38 per dose, and the economic delivery cost was $1.49 per dose. WHO has recommended the programmatic use of TCV in typhoid-endemic countries, and Gavi has included TCV in its vaccine portfolio. This first costing study of large-scale TCV introduction within a public sector immunization program provides empirical evidence for policymakers, stakeholders, and future vaccine campaign planning. |
Programmatic effectiveness of a pediatric typhoid conjugate vaccine campaign in Navi Mumbai, India
Hoffman SA , LeBoa C , Date K , Haldar P , Harvey P , Shimpi R , An Q , Zhang C , Jayaprasad N , Horng L , Fagerli K , Borhade P , Chakraborty D , Bahl S , Katkar A , Kunwar A , Yewale V , Andrews JR , Bhatnagar P , Dutta S , Luby SP . Clin Infect Dis 2023 BACKGROUND: The WHO recommends vaccines for prevention and control of typhoid fever, especially where antimicrobial-resistant typhoid circulates. In 2018 the Navi Mumbai Municipal Corporation (NMMC), implemented a TCV campaign. The campaign targeted all children aged 9-months through 14-years within NMMC boundaries (∼320,000 children) over 2 vaccination phases. The phase 1 campaign occurred from July 14-August 25, 2018 (71% coverage, ∼113,420 children). We evaluated the phase 1 campaign's programmatic effectiveness in reducing typhoid cases at the community level. METHODS: We established prospective, blood culture-based surveillance at 6 hospitals in Navi Mumbai, offering blood cultures to children presenting with fever ≥ 3 days. We employed a cluster-randomized (by administrative boundary) test-negative design to estimate the effectiveness of the vaccination campaign on pediatric typhoid cases. We matched test-positive, culture-confirmed typhoid cases with up to 3 test-negative, culture-negative controls by age and date of blood culture and assessed community vaccine campaign phase as an exposure using conditional logistic regression. RESULTS: Between September 1, 2018-March 31, 2021, we identified 81 typhoid cases and matched these with 238 controls. Cases were 0.44 times as likely to live in vaccine campaign communities (programmatic effectiveness, 56%, 95%CI: 25%-74%, p=0.002). Cases ≥ 5-years-old were 0.37 times as likely (95% CI: 0.19-0.70; p-value = 0.002) and cases during the first year of surveillance were 0.30 times as likely (95% CI: 0.14-0.64; p-value = 0.002) to live in vaccine campaign communities. CONCLUSIONS: Our findings support the use of TCV mass vaccination campaigns as effective population-based tools to combat typhoid fever. |
India field epidemiology training program response to COVID-19 pandemic, 2020-2021
Singh SK , Dikid T , Dhuria M , Bahl A , Chandra R , Pradeep VT , Prajapati SM , Nirwan N , Paul L , Murhekar M , Kaur P , Parasuraman G , Bhat P , Longkumer S , Dzeyie KA , Bhatnagar P , Minh NNT , Tanwar S , Yadav R , Desai M . Emerg Infect Dis 2022 28 (13) S138-s144 The India Field Epidemiology Training Program (FETP) has played a critical role in India's response to the ongoing COVID-19 pandemic. During March 2020-June 2021, a total of 123 FETP officers from across 3 training hubs were deployed in support of India's efforts to combat COVID-19. FETP officers have successfully mitigated the effect of COVID-19 on persons in India by conducting cluster outbreak investigations, performing surveillance system evaluations, and developing infection prevention and control tools and guidelines. This report discusses the successes of select COVID-19 pandemic response activities undertaken by current India FETP officers and proposes a pathway to augmenting India's pandemic preparedness and response efforts through expansion of this network and a strengthened frontline public health workforce. |
Progress toward measles and rubella elimination - India, 2005-2021
Murugan R , VanderEnde K , Dhawan V , Haldar P , Chatterjee S , Sharma D , Dzeyie KA , Pattabhiramaiah SB , Khanal S , Sangal L , Bahl S , Tanwar SSS , Morales M , Kassem AM . MMWR Morb Mortal Wkly Rep 2022 71 (50) 1569-1575 In 2019, India, along with other countries in the World Health Organization (WHO) South-East Asia Region,* adopted the goal of measles and rubella elimination by 2023,(†) a revision of the previous goal of measles elimination and control of rubella and congenital rubella syndrome (CRS) by 2020(§) (1-3). During 2017-2021, India adopted a national strategic plan for measles and rubella elimination (4), introduced rubella-containing vaccine (RCV) into the routine immunization program, launched a nationwide measles-rubella supplementary immunization activity (SIA) catch-up campaign, transitioned from outbreak-based surveillance to case-based acute fever and rash surveillance, and more than doubled the number of laboratories in the measles-rubella network, from 13 to 27. Strategies included 1) achieving and maintaining high population immunity with at least 95% vaccination coverage by providing 2 doses of measles- and rubella-containing vaccines; 2) ensuring a sensitive and timely case-based measles, rubella and CRS surveillance system; 3) maintaining an accredited measles and rubella laboratory network; 4) ensuring adequate outbreak preparedness and rapid response to measles and rubella outbreaks; and 5) strengthening support and linkages to achieve these strategies, including planning and progress monitoring, advocacy, social mobilization and communication, identification and utilization of synergistic linkages of integrated program efforts, research, and development. This report describes India's progress toward the elimination of measles and rubella during 2005-2021, with a focus on the years 2017-2021.(¶) During 2005-2021, coverage with the first dose of a measles-containing vaccine (MCV) administered through routine immunization increased 31%, from 68% to 89%. During 2011-2021, coverage with a second MCV dose (MCV2) increased by 204%, from 27% to 82%. During 2017-2021, coverage with a first dose of RCV (RCV1) increased almost 14-fold, from 6% to 89%. More than 324 million children received a measles- and rubella-containing vaccine (MRCV) during measles-rubella SIAs completed in 34 (94%) of 36 states and union territories (states) during 2017-2019. During 2017-2021, annual measles incidence decreased 62%, from 10.4 to 4.0 cases per 1 million population, and rubella incidence decreased 48%, from 2.3 to 1.2 cases per 1 million population. India has made substantial progress toward measles and rubella elimination; however, urgent and intensified efforts are required to achieve measles and rubella elimination by 2023. |
2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.
Kuhn JH , Adkins S , Alkhovsky SV , Avi-upanc T , Aylln MA , Bahl J , Balkema-Buschmann A , Ballinger MJ , Bandte M , Beer M , Bejerman N , Bergeron , Biedenkopf N , Bigarr L , Blair CD , Blasdell KR , Bradfute SB , Briese T , Brown PA , Bruggmann R , Buchholz UJ , Buchmeier MJ , Bukreyev A , Burt F , Bttner C , Calisher CH , Candresse T , Carson J , Casas I , Chandran K , Charrel RN , Chiaki Y , Crane A , Crane M , Dacheux L , B ED , delaTorre JC , deLamballerie X , deSouza WM , deSwart RL , Dheilly NM , DiPaola N , DiSerio F , Dietzgen RG , Digiaro M , Drexler JF , Duprex WP , Drrwald R , Easton AJ , Elbeaino T , Ergnay K , Feng G , Feuvrier C , Firth AE , Fooks AR , Formenty PBH , Freitas-Asta J , Gago-Zachert S , Garca ML , Garca-Sastre A , Garrison AR , Godwin SE , Gonzalez JJ , deBellocq JG , Griffiths A , Groschup MH , Gnther S , Hammond J , Hepojoki J , Hierweger MM , Hong S , Horie M , Horikawa H , Hughes HR , Hume AJ , Hyndman TH , Jing D , Jonson GB , Junglen S , Kadono F , Karlin DG , Klempa B , Klingstrm J , Koch MC , Kond H , Koonin EV , Krsov J , Krupovic M , Kubota K , Kuzmin IV , Laenen L , Lambert AJ , L J , Li JM , Lieffrig F , Lukashevich IS , Luo D , Maes P , Marklewitz M , Marshall SH , Marzano SL , McCauley JW , Mirazimi A , Mohr PG , Moody NJG , Morita Y , Morrison RN , Mhlberger E , Naidu R , Natsuaki T , Navarro JA , Neriya Y , Netesov SV , Neumann G , Nowotny N , Ochoa-Corona FM , Palacios G , Pallandre L , Palls V , Papa A , Paraskevopoulou S , Parrish CR , Pauvolid-Corra A , Pawska JT , Prez DR , Pfaff F , Plemper RK , Postler TS , Pozet F , Radoshitzky SR , Ramos-Gonzlez PL , Rehanek M , Resende RO , Reyes CA , Romanowski V , Rubbenstroth D , Rubino L , Rumbou A , Runstadler JA , Rupp M , Sabanadzovic S , Sasaya T , Schmidt-Posthaus H , Schwemmle M , Seuberlich T , Sharpe SR , Shi M , Sironi M , Smither S , Song JW , Spann KM , Spengler JR , Stenglein MD , Takada A , Tesh RB , Tkov J , Thornburg NJ , Tischler ND , Tomitaka Y , Tomonaga K , Tordo N , Tsunekawa K , Turina M , Tzanetakis IE , Vaira AM , vandenHoogen B , Vanmechelen B , Vasilakis N , Verbeek M , vonBargen S , Wada J , Wahl V , Walker PJ , Whitfield AE , Williams JV , Wolf YI , Yamasaki J , Yanagisawa H , Ye G , Zhang YZ , kland AL . Arch Virol 2022 167 (12) 2857-2906 In March 2022, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by two new families (bunyaviral Discoviridae and Tulasviridae), 41 new genera, and 98 new species. Three hundred forty-nine species were renamed and/or moved. The accidentally misspelled names of seven species were corrected. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV. |
Progress toward measles elimination - South-East Asia Region, 2003-2020
Khanal S , Kassem AM , Bahl S , Jayantha L , Sangal L , Sharfuzzaman M , Bose AS , Antoni S , Datta D , Alexander JPJr . MMWR Morb Mortal Wkly Rep 2022 71 (33) 1042-1046 In 2013, member states of the World Health Organization (WHO) South-East Asia Region* (SEAR) adopted the goal of measles elimination and rubella and congenital rubella syndrome control(†) by 2020 (1). In 2014, to provide impetus toward achieving this goal, the Regional Director declared measles elimination and rubella control one of the Regional Flagship Priorities. In 2019, SEAR member states declared a revised goal of eliminating both measles and rubella(§) by 2023 (2). The recommended strategies to achieve elimination include 1) achieving and maintaining ≥95% coverage with 2 doses of measles- and rubella-containing vaccine in every district through routine or supplementary immunization activities(¶) (SIAs); 2) developing and sustaining a sensitive and timely case-based surveillance system that meets recommended performance indicators**; 3) developing and maintaining an accredited laboratory network; 4) achieving timely identification, investigation, and response to measles outbreaks; and 5) collaborating with other public health initiatives to achieve the preceding four strategies. This report updates a previous report and describes progress toward measles elimination in SEAR during 2003-2020 (3). In 2002, coverage with the first dose of a measles-containing vaccine in routine immunization (MCV1) was 70%, and only three countries in SEAR had added a second routine dose of measles-containing vaccine in routine immunization (MCV2). During 2003-2020, all countries introduced MCV2, and estimated coverage with MCV1 increased 35%, from 65% to 88%, and coverage with MCV2 increased 1,233% from 6% to 80%. Approximately 938 million persons were vaccinated in SIAs. Annual reported measles incidence declined by 92%, from 57.0 to 4.8 cases per 1 million population, and estimated deaths decreased by 97%; an estimated 9.3 million deaths were averted by measles vaccination. By 2020, five countries were verified as having achieved measles elimination. To achieve measles elimination in the region by 2023, additional efforts are urgently needed to strengthen routine immunization services and improve measles-containing vaccine (MCV) coverage, conduct periodic high-quality SIAs, and strengthen measles case-based surveillance and laboratory capacity. |
Novel and extendable genotyping system for human respiratory syncytial virus based on whole-genome sequence analysis.
Chen J , Qiu X , Avadhanula V , Shepard SS , Kim DK , Hixson J , Piedra PA , Bahl J . Influenza Other Respir Viruses 2021 16 (3) 492-500 BACKGROUND: Human respiratory syncytial virus (RSV) is one of the leading causes of respiratory infections, especially in infants and young children. Previous RSV sequencing studies have primarily focused on partial sequencing of G gene (200-300 nucleotides) for genotype characterization or diagnostics. However, the genotype assignment with G gene has not recapitulated the phylogenetic signal of other genes, and there is no consensus on RSV genotype definition. METHODS: We conducted maximum likelihood phylogenetic analysis with 10 RSV individual genes and whole-genome sequence (WGS) that are published in GenBank. RSV genotypes were determined by using phylogenetic analysis and pair-wise node distances. RESULTS: In this study, we first statistically examined the phylogenetic incongruence, rate variation for each RSV gene sequence and WGS. We then proposed a new RSV genotyping system based on a comparative analysis of WGS and the temporal distribution of strains. We also provide an RSV classification tool to perform RSV genotype assignment and a publicly accessible up-to-date instance of Nextstrain where the phylogenetic relationship of all genotypes can be explored. CONCLUSIONS: This revised RSV genotyping system will provide important information for disease surveillance, epidemiology, and vaccine development. |
2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.
Kuhn JH , Adkins S , Agwanda BR , Al Kubrusli R , Alkhovsky Aльxoвcкий Cepгeй Bлaдимиpoвич SV , Amarasinghe GK , Avšič-Županc T , Ayllón MA , Bahl J , Balkema-Buschmann A , Ballinger MJ , Basler CF , Bavari S , Beer M , Bejerman N , Bennett AJ , Bente DA , Bergeron É , Bird BH , Blair CD , Blasdell KR , Blystad DR , Bojko J , Borth WB , Bradfute S , Breyta R , Briese T , Brown PA , Brown JK , Buchholz UJ , Buchmeier MJ , Bukreyev A , Burt F , Büttner C , Calisher CH , Cao 曹孟籍 M , Casas I , Chandran K , Charrel RN , Cheng Q , Chiaki 千秋祐也 Y , Chiapello M , Choi IR , Ciuffo M , Clegg JCS , Crozier I , Dal Bó E , de la Torre JC , de Lamballerie X , de Swart RL , Debat H , Dheilly NM , Di Cicco E , Di Paola N , Di Serio F , Dietzgen RG , Digiaro M , Dolnik O , Drebot MA , Drexler JF , Dundon WG , Duprex WP , Dürrwald R , Dye JM , Easton AJ , Ebihara 海老原秀喜 H , Elbeaino T , Ergünay K , Ferguson HW , Fooks AR , Forgia M , Formenty PBH , Fránová J , Freitas-Astúa J , Fu 付晶晶 J , Fürl S , Gago-Zachert S , Gāo 高福 GF , García ML , García-Sastre A , Garrison AR , Gaskin T , Gonzalez JJ , Griffiths A , Goldberg TL , Groschup MH , Günther S , Hall RA , Hammond J , Han 韩彤 T , Hepojoki J , Hewson R , Hong 洪健 J , Hong 洪霓 N , Hongo 本郷誠治 S , Horie 堀江真行 M , Hu JS , Hu T , Hughes HR , Hüttner F , Hyndman TH , Ilyas M , Jalkanen R , Jiāng 姜道宏 D , Jonson GB , Junglen S , Kadono 上遠野冨士夫 F , Kaukinen KH , Kawate M , Klempa B , Klingström J , Kobinger G , Koloniuk I , Kondō 近藤秀樹 H , Koonin EV , Krupovic M , Kubota 久保田健嗣 K , Kurath G , Laenen L , Lambert AJ , Langevin SL , Lee B , Lefkowitz EJ , Leroy EM , Li 李邵蓉 S , Li 李龙辉 L , Lǐ 李建荣 J , Liu 刘华珍 H , Lukashevich IS , Maes P , de Souza WM , Marklewitz M , Marshall SH , Marzano SL , Massart S , McCauley JW , Melzer M , Mielke-Ehret N , Miller KM , Ming TJ , Mirazimi A , Mordecai GJ , Mühlbach HP , Mühlberger E , Naidu R , Natsuaki 夏秋知英 T , Navarro JA , Netesov Heтёcoв Cepгeй Bиктopoвич SV , Neumann G , Nowotny N , Nunes MRT , Olmedo-Velarde A , Palacios G , Pallás V , Pályi B , Papa Άννα Παπά A , Paraskevopoulou Σοφία Παρασκευοπούλου S , Park AC , Parrish CR , Patterson DA , Pauvolid-Corrêa A , Pawęska JT , Payne S , Peracchio C , Pérez DR , Postler TS , Qi 亓立莹 L , Radoshitzky SR , Resende RO , Reyes CA , Rima BK , Luna GR , Romanowski V , Rota P , Rubbenstroth D , Rubino L , Runstadler JA , Sabanadzovic S , Sall AA , Salvato MS , Sang R , Sasaya 笹谷孝英 T , Schulze AD , Schwemmle M , Shi 施莽 M , Shí 石晓宏 X , Shí 石正丽 Z , Shimomoto 下元祥史 Y , Shirako Y , Siddell SG , Simmonds P , Sironi M , Smagghe G , Smither S , Song 송진원 JW , Spann K , Spengler JR , Stenglein MD , Stone DM , Sugano J , Suttle CA , Tabata A , Takada 高田礼人 A , Takeuchi 竹内繁治 S , Tchouassi DP , Teffer A , Tesh RB , Thornburg NJ , Tomitaka 冨高保弘 Y , Tomonaga 朝長啓造 K , Tordo N , Torto B , Towner JS , Tsuda 津田新哉 S , Tu 涂长春 C , Turina M , Tzanetakis IE , Uchida J , Usugi 宇杉富雄 T , Vaira AM , Vallino M , van den Hoogen B , Varsani A , Vasilakis Νίκος Βασιλάκης N , Verbeek M , von Bargen S , Wada 和田治郎 J , Wahl V , Walker PJ , Wang 王林发 LF , Wang 王国平 G , Wang 王雁翔 Y , Wang 王亚琴 Y , Waqas M , Wèi 魏太云 T , Wen 温少华 S , Whitfield AE , Williams JV , Wolf YI , Wu 吴建祥 J , Xu 徐雷 L , Yanagisawa 栁澤広宣 H , Yang 杨彩霞 C , Yang 杨作坤 Z , Zerbini FM , Zhai 翟立峰 L , Zhang 张永振 YZ , Zhang 张松 S , Zhang 张靖国 J , Zhang 张哲 Z , Zhou 周雪平 X . Arch Virol 2021 166 (12) 3513-3566 In March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV. |
Proposal for Human Respiratory Syncytial Virus Nomenclature below the Species Level.
Salimi V , Viegas M , Trento A , Agoti CN , Anderson LJ , Avadhanula V , Bahl J , Bont L , Brister JR , Cane PA , Galiano M , Graham BS , Hatcher EL , Hellferscee O , Henke DM , Hirve S , Jackson S , Keyaerts E , Kragten-Tabatabaie L , Lindstrom S , Nauwelaers I , Nokes DJ , Openshaw PJ , Peret TC , Piedra PA , Ramaekers K , Rector A , Trovão NS , von Gottberg A , Zambon M , Zhang W , Williams TC , Barr IG , Buchholz UJ . Emerg Infect Dis 2021 27 (6) 1-9 Human respiratory syncytial virus (HRSV) is the leading viral cause of serious pediatric respiratory disease, and lifelong reinfections are common. Its 2 major subgroups, A and B, exhibit some antigenic variability, enabling HRSV to circulate annually. Globally, research has increased the number of HRSV genomic sequences available. To ensure accurate molecular epidemiology analyses, we propose a uniform nomenclature for HRSV-positive samples and isolates, and HRSV sequences, namely: HRSV/subgroup identifier/geographic identifier/unique sequence identifier/year of sampling. We also propose a template for submitting associated metadata. Universal nomenclature would help researchers retrieve and analyze sequence data to better understand the evolution of this virus. |
2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.
Kuhn JH , Adkins S , Alioto D , Alkhovsky SV , Amarasinghe GK , Anthony SJ , Avšič-Županc T , Ayllón MA , Bahl J , Balkema-Buschmann A , Ballinger MJ , Bartonička T , Basler C , Bavari S , Beer M , Bente DA , Bergeron É , Bird BH , Blair C , Blasdell KR , Bradfute SB , Breyta R , Briese T , Brown PA , Buchholz UJ , Buchmeier MJ , Bukreyev A , Burt F , Buzkan N , Calisher CH , Cao M , Casas I , Chamberlain J , Chandran K , Charrel RN , Chen B , Chiumenti M , Choi IR , Clegg JCS , Crozier I , da Graça JV , Dal Bó E , Dávila AMR , de la Torre JC , de Lamballerie X , de Swart RL , Di Bello PL , Di Paola N , Di Serio F , Dietzgen RG , Digiaro M , Dolja VV , Dolnik O , Drebot MA , Drexler JF , Dürrwald R , Dufkova L , Dundon WG , Duprex WP , Dye JM , Easton AJ , Ebihara H , Elbeaino T , Ergünay K , Fernandes J , Fooks AR , Formenty PBH , Forth LF , Fouchier RAM , Freitas-Astúa J , Gago-Zachert S , Gāo GF , García ML , García-Sastre A , Garrison AR , Gbakima A , Goldstein T , Gonzalez JJ , Griffiths A , Groschup MH , Günther S , Guterres A , Hall RA , Hammond J , Hassan M , Hepojoki J , Hepojoki S , Hetzel U , Hewson R , Hoffmann B , Hongo S , Höper D , Horie M , Hughes HR , Hyndman TH , Jambai A , Jardim R , Jiāng D , Jin Q , Jonson GB , Junglen S , Karadağ S , Keller KE , Klempa B , Klingström J , Kobinger G , Kondō H , Koonin EV , Krupovic M , Kurath G , Kuzmin IV , Laenen L , Lamb RA , Lambert AJ , Langevin SL , Lee B , Lemos ERS , Leroy EM , Li D , Lǐ J , Liang M , Liú W , Liú Y , Lukashevich IS , Maes P , Marciel de Souza W , Marklewitz M , Marshall SH , Martelli GP , Martin RR , Marzano SL , Massart S , McCauley JW , Mielke-Ehret N , Minafra A , Minutolo M , Mirazimi A , Mühlbach HP , Mühlberger E , Naidu R , Natsuaki T , Navarro B , Navarro JA , Netesov SV , Neumann G , Nowotny N , Nunes MRT , Nylund A , Økland AL , Oliveira RC , Palacios G , Pallas V , Pályi B , Papa A , Parrish CR , Pauvolid-Corrêa A , Pawęska JT , Payne S , Pérez DR , Pfaff F , Radoshitzky SR , Rahman AU , Ramos-González PL , Resende RO , Reyes CA , Rima BK , Romanowski V , Robles Luna G , Rota P , Rubbenstroth D , Runstadler JA , Ruzek D , Sabanadzovic S , Salát J , Sall AA , Salvato MS , Sarpkaya K , Sasaya T , Schwemmle M , Shabbir MZ , Shí X , Shí Z , Shirako Y , Simmonds P , Širmarová J , Sironi M , Smither S , Smura T , Song JW , Spann KM , Spengler JR , Stenglein MD , Stone DM , Straková P , Takada A , Tesh RB , Thornburg NJ , Tomonaga K , Tordo N , Towner JS , Turina M , Tzanetakis I , Ulrich RG , Vaira AM , van den Hoogen B , Varsani A , Vasilakis N , Verbeek M , Wahl V , Walker PJ , Wang H , Wang J , Wang X , Wang LF , Wèi T , Wells H , Whitfield AE , Williams JV , Wolf YI , Wú Z , Yang X , Yáng X , Yu X , Yutin N , Zerbini FM , Zhang T , Zhang YZ , Zhou G , Zhou X . Arch Virol 2020 165 (12) 3023-3072 In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV. |
Decision making and implementation of the first public sector introduction of typhoid conjugate vaccine - Navi Mumbai, India, 2018
Date K , Shimpi R , Luby S , N R , Haldar P , Katkar A , Wannemuehler K , Mogasale V , Pallas S , Song D , Kunwar A , Loharikar A , Yewale V , Ahmed D , Horng L , Wilhelm E , Bahl S , Harvey P , Dutta S , Bhatnagar P . Clin Infect Dis 2020 71 S172-s178 BACKGROUND: Typhoid fever prevention and control efforts are critical in an era of rising antimicrobial resistance among typhoid pathogens. India remains one of the highest typhoid disease burden countries, although a highly efficacious typhoid conjugate vaccine (TCV), prequalified by the World Health Organization in 2017, has been available since 2013. In 2018, the Navi Mumbai Municipal Corporation (NMMC) introduced TCV into its immunization program, targeting children aged 9 months to 14 years in 11 of 22 areas (Phase 1 campaign). We describe the decision making, implementation, and delivery costing to inform TCV use in other settings. METHODS: We collected information on the decision making and campaign implementation in addition to administrative coverage from NMMC and partners. We then used a microcosting approach from the local government (NMMC) perspective, using a new Microsoft Excel-based tool to estimate the financial and economic vaccination campaign costs. RESULTS: The planning and implementation of the campaign were led by NMMC with support from multiple partners. A fixed-post campaign was conducted during weekends and public holidays in July-August 2018 which achieved an administrative vaccination coverage of 71% (ranging from 46% in high-income to 92% in low-income areas). Not including vaccine and vaccination supplies, the average financial cost and economic cost per dose of TCV delivery were $0.45 and $1.42, respectively. CONCLUSION: The first public sector TCV campaign was successfully implemented by NMMC, with high administrative coverage in slums and low-income areas. Delivery cost estimates provide important inputs to evaluate the cost-effectiveness and affordability of TCV vaccination through public sector preventive campaigns. |
Developing standardized competencies to strengthen immunization systems and workforce
Traicoff D , Pope A , Bloland P , Lal D , Bahl J , Stewart S , Ryman T , Abbruzzese M , Lee C , Ahrendts J , Shamalla L , Sandhu H . Vaccine 2019 37 (11) 1428-1435 Despite global support for immunization as a core component of the human right to health and the maturity of immunization programs in low- and middle-income countries throughout the world, there is no comprehensive description of the standardized competencies needed for immunization programs at the national, multiple sub-national, and community levels. The lack of defined and standardized competencies means countries have few guidelines to help them address immunization workforce planning, program management, and performance monitoring. Potential consequences resulting from the lack of defined competencies include inadequate or inefficient distribution of resources to support the required functions and difficulties in adequately managing the health workforce. In 2015, an international multi-agency working group convened to define standardized competencies that national immunization programs could adapt for their own workforce planning needs. The working group used a stepwise approach to ensure that the competencies would align with immunization programs' objectives. The first step defined the attributes of a successful immunization program. The group then defined the work functions needed to achieve those attributes. Based on the work functions, the working group defined specific competencies. This process resulted in three products: (1) Attributes of an immunization program described within eight technical domains at four levels within a health system: National, Provincial, District/Local, and Community; (2) 229 distinct functions within those eight domains at each of the four levels; and (3) 242 competencies, representing eight technical domains and two foundational domains (Management and Leadership and Vaccine Preventable Diseases and Program). Currently available as a working draft and being tested with immunization projects in several countries, the final document will be published by WHO as normative guidelines. Vertical immunization programs as well as integrated systems can customize the framework to suit their needs. Standardized competencies can support immunization program improvements and help strengthen effective health systems. |
Measles-rubella supplementary immunization activity readiness assessment - India, 2017-2018
Gurnani V , Haldar P , Khanal S , Bhatnagar P , Singh B , Ahmed D , Samiuddin M , Kumar A , Negi Y , Gupta S , Harvey P , Bahl S , Dabbagh A , Alexander JP , Goodson JL . MMWR Morb Mortal Wkly Rep 2018 67 (26) 742-746 In 2013, during the 66th session of the Regional Committee of the World Health Organization (WHO) South-East Asia Region (SEAR), the 11 SEAR countries* adopted goals to eliminate measles and control rubella and congenital rubella syndrome by 2020(dagger) (1). To accelerate progress in India (2,3), a phased( section sign) nationwide supplementary immunization activity (SIA)( paragraph sign) using measles-rubella vaccine and targeting approximately 410 million children aged 9 months-14 years commenced in 2017 and will be completed by first quarter of 2019. To ensure a high-quality SIA, planning and preparation were monitored using a readiness assessment tool adapted from the WHO global field guide** (4) by the India Ministry of Health and Family Welfare. This report describes the results and experience gained from conducting SIA readiness assessments in 24 districts of three Indian states (Andhra Pradesh, Kerala, and Telangana) during the second phase of the SIA. In each selected area, assessments were conducted 4-6 weeks and 1-2 weeks before the scheduled SIA. At the first assessment, none of the states and districts were on track with preparations for the SIA. However, at the second assessment, two (67%) states and 21 (88%) districts were on track. The SIA readiness assessment identified several preparedness gaps; early assessment results were immediately communicated to authorities and led to necessary corrective actions to ensure high-quality SIA implementation. |
Progress toward rubella and congenital rubella syndrome control - South-East Asia Region, 2000-2016
Khanal S , Bahl S , Sharifuzzaman M , Dhongde D , Pattamadilok S , Reef S , Morales M , Dabbagh A , Kretsinger K , Patel M . MMWR Morb Mortal Wkly Rep 2018 67 (21) 602-606 In 2013, the 66th session of the Regional Committee of the World Health Organization (WHO) South-East Asia Region (SEAR)* adopted the goal of elimination of measles and control(dagger) of rubella and congenital rubella syndrome (CRS) by 2020 (1). Rubella is the leading vaccine-preventable cause of birth defects. Although rubella typically causes a mild fever and rash in children and adults, rubella virus infection during pregnancy, especially during the first trimester, can result in miscarriage, fetal death, or a constellation of congenital malformations known as CRS, commonly including visual, auditory, and/or cardiac defects, and developmental delay (2). Rubella and CRS control capitalizes on the momentum created by pursuing measles elimination because the efforts are programmatically linked. Rubella-containing vaccine (RCV) is administered as a combined measles and rubella vaccine, and rubella cases are detected through case-based surveillance for measles or fever and rash illness (3). This report summarizes progress toward rubella and CRS control in SEAR during 2000-2016. Estimated coverage with a first RCV dose (RCV1) increased from 3% of the birth cohort in 2000 to 15% in 2016 because of RCV introduction in six countries. RCV1 coverage is expected to increase rapidly with the phased introduction of RCV in India and Indonesia beginning in 2017; these countries are home to 83% of the SEAR birth cohort. During 2000-2016, approximately 83 million persons were vaccinated through 13 supplemental immunization activities (SIAs) conducted in eight countries. During 2010-2016, reported rubella incidence decreased by 37%, from 8.6 to 5.4 cases per 1 million population, and four countries (Bangladesh, Maldives, Sri Lanka, and Thailand) reported a decrease in incidence of >/=95% since 2010. To achieve rubella and CRS control in SEAR, sustained investment to increase routine RCV coverage, periodic high-quality SIAs to close immunity gaps, and strengthened rubella and CRS surveillance are needed. |
Progress toward measles elimination - Bangladesh, 2000-2016
Khanal S , Bohara R , Chacko S , Sharifuzzaman M , Shamsuzzaman M , Goodson JL , Dabbagh A , Kretsinger K , Dhongde D , Liyanage J , Bahl S , Thapa A . MMWR Morb Mortal Wkly Rep 2017 66 (28) 753-757 In 2013, at the 66th session of the Regional Committee of the World Health Organization (WHO) South-East Asia Region (SEAR), a regional goal was established to eliminate measles and control rubella and congenital rubella syndrome* by 2020 (1). WHO-recommended measles elimination strategies in SEAR countries include 1) achieving and maintaining ≥95% coverage with 2 doses of measles-containing vaccine (MCV) in every district, delivered through the routine immunization program or through supplementary immunization activities (SIAs)dagger; 2) developing and sustaining a sensitive and timely measles case-based surveillance system that meets targets for recommended performance indicators; and 3) developing and maintaining an accredited measles laboratory network (2). In 2014, Bangladesh, one of 11 countries in SEAR, adopted a national goal for measles elimination by 2018 (2,3). This report describes progress and challenges toward measles elimination in Bangladesh during 2000-2016. Estimated coverage with the first MCV dose (MCV1) increased from 74% in 2000 to 94% in 2016. The second MCV dose (MCV2) was introduced in 2012, and MCV2 coverage increased from 35% in 2013 to 93% in 2016. During 2000-2016, approximately 108.9 million children received MCV during three nationwide SIAs conducted in phases. During 2000-2016, reported confirmed measles incidence decreased 82%, from 34.2 to 6.1 per million population. However, in 2016, 56% of districts did not meet the surveillance performance target of ≥2 discarded nonmeasles, nonrubella cases section sign per 100,000 population. Additional measures that include increasing MCV1 and MCV2 coverage to ≥95% in all districts with additional strategies for hard-to-reach populations, increasing sensitivity of measles case-based surveillance, and ensuring timely transport of specimens to the national laboratory will help achieve measles elimination. |
Japanese encephalitis surveillance and immunization - Asia and Western Pacific Regions, 2016
Heffelfinger JD , Li X , Batmunkh N , Grabovac V , Diorditsa S , Liyanage JB , Pattamadilok S , Bahl S , Vannice KS , Hyde TB , Chu SY , Fox KK , Hills SL , Marfin AA . MMWR Morb Mortal Wkly Rep 2017 66 (22) 579-583 Japanese encephalitis (JE) virus is the most important vaccine-preventable cause of encephalitis in the Asia-Pacific region. The World Health Organization (WHO) recommends integration of JE vaccination into national immunization schedules in all areas where the disease is a public health priority (1). This report updates a previous summary of JE surveillance and immunization programs in Asia and the Western Pacific in 2012 (2). Since 2012, funding for JE immunization has become available through the GAVI Alliance, three JE vaccines have been WHO-prequalified,* and an updated WHO JE vaccine position paper providing guidance on JE vaccines and vaccination strategies has been published (1). Data for this report were obtained from a survey of JE surveillance and immunization practices administered to health officials in countries with JE virus transmission risk, the 2015 WHO/United Nations Children's Fund Joint Reporting Form on Immunization, notes and reports from JE meetings held during 2014-2016, published literature, and websites. In 2016, 22 (92%) of 24 countries with JE virus transmission risk conducted JE surveillance, an increase from 18 (75%) countries in 2012, and 12 (50%) countries had a JE immunization program, compared with 11 (46%) countries in 2012. Strengthened JE surveillance, continued commitment, and adequate resources for JE vaccination should help maintain progress toward prevention and control of JE. |
Notes from the field: Detection of Sabin-like type 2 poliovirus from sewage after global cessation of trivalent oral poliovirus vaccine - Hyderabad and Ahmedabad, India, August-September 2016
Bahl S , Hampton LM , Bhatnagar P , Rao GS , Haldar P , Sangal L , Jetty PA , Nalavade UP . MMWR Morb Mortal Wkly Rep 2017 65 (52) 1493-1494 During September 2–October 4, 2016, four sewage samples collected during August 3–September 19 (Hyderabad, Telangana State, India) and one sewage sample collected on August 30 (Ahmedabad, Gujarat State, India) tested positive for Sabin-like type 2 polioviruses. These polioviruses were detected approximately 4 months after April 25, 2016, when India officially ceased use of trivalent oral poliovirus vaccine (tOPV), containing Sabin attenuated types 1, 2, and 3 polioviruses, and switched to bivalent OPV (bOPV), containing Sabin attenuated types 1 and 3 polioviruses (1). | Detection of Sabin-like type 2 poliovirus approximately 4 months after the switch from tOPV to bOPV suggested that tOPV use might have continued after it was supposed to stop globally, creating a risk for emergence of new type 2 vaccine-derived polioviruses (VDPV2s), which can cause paralysis. Genetic sequencing of the 903-nucleotide VP1 region of the isolated viruses showed zero, one, two, and four nucleotide changes in the four Hyderabad isolates and one nucleotide change in the Ahmedabad isolate, compared with the type 2 polioviruses in tOPV. These findings indicated that the isolated polioviruses had not replicated sufficiently to accumulate more than a few mutations on a potential pathway to becoming VDPV2s, and that the tOPV they originated from had likely been used during the preceding 4 months. | In accordance with global guidelines for responding to poliovirus events (2), detailed investigations were initiated within 48 hours of detection of the type 2 poliovirus in Hyderabad and the neighboring Rangareddy district, and in Ahmedabad (Box). As part of global poliovirus containment efforts (3), laboratories in those areas potentially storing type 2 polioviruses had previously been found to not have such polioviruses, so they were not searched. Telangana and Gujarat state officials met with immunization program stakeholders in the affected districts and other districts in their states regarding the need to reconfirm withdrawal of all tOPV. |
Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler.
Shepard SS , Meno S , Bahl J , Wilson MM , Barnes J , Neuhaus E . BMC Genomics 2016 17 (1) 708 BACKGROUND: Deep sequencing makes it possible to observe low-frequency viral variants and sub-populations with greater accuracy and sensitivity than ever before. Existing platforms can be used to multiplex a large number of samples; however, analysis of the resulting data is complex and involves separating barcoded samples and various read manipulation processes ending in final assembly. Many assembly tools were designed with larger genomes and higher fidelity polymerases in mind and do not perform well with reads derived from highly variable viral genomes. Reference-based assemblers may leave gaps in viral assemblies while de novo assemblers may struggle to assemble unique genomes. RESULTS: The IRMA (iterative refinement meta-assembler) pipeline solves the problem of viral variation by the iterative optimization of read gathering and assembly. As with all reference-based assembly, reads are included in assembly when they match consensus template sets; however, IRMA provides for on-the-fly reference editing, correction, and optional elongation without the need for additional reference selection. This increases both read depth and breadth. IRMA also focuses on quality control, error correction, indel reporting, variant calling and variant phasing. In fact, IRMA's ability to detect and phase minor variants is one of its most distinguishing features. We have built modules for influenza and ebolavirus. We demonstrate usage and provide calibration data from mixture experiments. Methods for variant calling, phasing, and error estimation/correction have been redesigned to meet the needs of viral genomic sequencing. CONCLUSION: IRMA provides a robust next-generation sequencing assembly solution that is adapted to the needs and characteristics of viral genomes. The software solves issues related to the genetic diversity of viruses while providing customized variant calling, phasing, and quality control. IRMA is freely available for non-commercial use on Linux and Mac OS X and has been parallelized for high-throughput computing. |
Fractional-dose inactivated poliovirus vaccine immunization campaign - Telangana state, India, June 2016
Bahl S , Verma H , Bhatnagar P , Haldar P , Satapathy A , Kumar KN , Horton J , Estivariz CF , Anand A , Sutter R . MMWR Morb Mortal Wkly Rep 2016 65 (33) 859-863 Wild poliovirus type 2 was declared eradicated in September 2015 (1). In April 2016, India, switched from use of trivalent oral poliovirus vaccine (tOPV; containing types 1, 2, and 3 polio vaccine viruses), to bivalent OPV (bOPV; containing types 1 and 3), as part of a globally synchronized initiative to withdraw Sabin poliovirus type 2 vaccine. Concurrently, inactivated poliovirus vaccine (IPV) was introduced into India's routine immunization program to maintain an immunity base that would mitigate the number of paralytic cases in the event of epidemic transmission of poliovirus type 2 (2,3). After cessation of use of type 2 Sabin vaccine, any reported isolation of vaccine-derived poliovirus type 2 (VDPV2) would be treated as a public health emergency and might need outbreak response with monovalent type 2 oral vaccine, IPV, or both (4). In response to identification of a VDPV2 isolate from a sewage sample collected in the southern state of Telangana in May 2016, India conducted a mass vaccination campaign in June 2016 using an intradermal fractional dose (0.1 ml) of IPV (fIPV). Because of a global IPV supply shortage, fIPV, which uses one fifth of regular intramuscular (IM) dose administered intradermally, has been recommended as a response strategy for VDPV2 (5). Clinical trials have demonstrated that fIPV is highly immunogenic (6,7). During the 6-day campaign, 311,064 children aged 6 weeks-3 years were vaccinated, achieving an estimated coverage of 94%. With appropriate preparation, an emergency fIPV response can be promptly and successfully implemented. Lessons learned from this campaign can be applied to successful implementation of future outbreak responses using fIPV. |
Cluster survey evaluation of a measles vaccination campaign in Jharkhand, India, 2012
Scobie HM , Ray A , Routray S , Bose A , Bahl S , Sosler S , Wannemuehler K , Kumar R , Haldar P , Anand A . PLoS One 2015 10 (5) e0127105 INTRODUCTION: India was the last country in the world to implement a two-dose strategy for measles-containing vaccine (MCV) in 2010. As part of measles second-dose introduction, phased measles vaccination campaigns were conducted during 2010-2013, targeting 131 million children 9 months to <10 years of age. We performed a post-campaign coverage survey to estimate measles vaccination coverage in Jharkhand state. METHODS: A multi-stage cluster survey was conducted 2 months after the phase 2 measles campaign occurred in 19 of 24 districts of Jharkhand during November 2011-March 2012. Vaccination status of children 9 months to <10 years of age was documented based on vaccination card or mother's recall. Coverage estimates and 95% confidence intervals (95% CI) for 1,018 children were calculated using survey methods. RESULTS: In the Jharkhand phase 2 campaign, MCV coverage among children aged 9 months to <10 years was 61.0% (95% CI: 54.4-67.7%). Significant differences in coverage were observed between rural (65.0%; 95% CI: 56.8-73.2%) and urban areas (45.6%; 95% CI: 37.3-53.9%). Campaign awareness among mothers was low (51.5%), and the most commonly reported reason for non-vaccination was being unaware of the campaign (69.4%). At the end of the campaign, 53.7% (95% CI: 46.5-60.9%) of children 12 months to <10 years of age received ≥2 MCV doses, while a large proportion of children remained under-vaccinated (34.0%, 95% CI: 28.0-40.0%) or unvaccinated (12.3%, 95% CI: 9.3-16.2%). CONCLUSIONS: Implementation of the national measles campaign was a significant achievement towards measles elimination in India. In Jharkhand, campaign performance was below the target coverage of ≥90% set by the Government of India, and challenges in disseminating campaign messages were identified. Efforts towards increasing two-dose MCV coverage are needed to achieve the recently adopted measles elimination goal in India and the South-East Asia region. |
Revised and updated nomenclature for highly pathogenic avian influenza A (H5N1) viruses
World Health Organization/World Organisation for Animal Health/Food and Agriculture Organization (WHO/OIE/FAO) H5N1 Evolution Working Group , Donis RO , Bahl J , Cox N , Davis CT , Jang Y , Shepard S . Influenza Other Respir Viruses 2014 8 (3) 384-8 The divergence of the hemagglutinin gene of A/goose/Guangdong/1/1996-lineage H5N1 viruses during 2011 and 2012 (807 new sequences collected through December 31, 2012) was analyzed by phylogenetic and p-distance methods to define new clades using the pre-established nomenclature system. Eight new clade designations were recommended based on division of clade 1·1 (Mekong River Delta), 2·1·3·2 (Indonesia), 2·2·2 (India/Bangladesh), 2·2·1·1 (Egypt/Israel), and 2·3·2·1 (Asia). A simplification to the previously defined criteria, which adds a letter rather than number to the right-most digit of fifth-order clades, was proposed to facilitate this and future updates. |
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