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3. Sensitive poliovirus detection using nested PCR and nanopore sequencing: a prospective validation study

Author

Shaw, Alexander G., Mampuela, Tresor Kabeya, Lofiko, Emmanuel Lokilo, Pratt, Catherine, Troman, Catherine, Bujaki, Erika, O’Toole, Áine, Akello, Joyce Odeke, Aziza, Adrienne Amuri, Lusamaki, Eddy Kinganda, Makangara, Jean Claude, Akonga, Marceline, Lay, Yvonne, Nsunda, Bibiche, White, Bailey, Jorgensen, David, Pukuta, Elizabeth, Riziki, Yogolelo, Rankin, Kathleen E., Rambaut, Andrew, Ahuka-Mundeke, Steve, Muyembe, Jean-Jacques, Martin, Javier, Grassly, Nicholas C., and Mbala-Kingebeni, Placide

Published
2023
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5. Sustained detection of type 2 poliovirus in London sewage between February and July, 2022, by enhanced environmental surveillance

Author

Klapsa, Dimitra, Wilton, Thomas, Zealand, Andrew, Bujaki, Erika, Saxentoff, Eugene, Troman, Catherine, Shaw, Alexander G, Tedcastle, Alison, Majumdar, Manasi, Mate, Ryan, Akello, Joyce O, Huseynov, Shahin, Zeb, Ali, Zambon, Maria, Bell, Anita, Hagan, José, Wade, Matthew J, Ramsay, Mary, Grassly, Nicholas C, Saliba, Vanessa, and Martin, Javier

Published
2022
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6. Enterovirus A71 and coxsackievirus A6 circulation in England, UK, 2006–2017: A mathematical modelling study using cross-sectional seroprevalence data.

Author

Kamau, Everlyn, Lambert, Ben, Allen, David J., Celma, Cristina, Beard, Stuart, Harvala, Heli, Simmonds, Peter, Grassly, Nicholas C., and Pons-Salort, Margarita

Subjects
FOOT & mouth disease, SEROPREVALENCE, ENTEROVIRUSES, NUMBER systems, ENTEROVIRUS diseases, SYMPTOMS, COXSACKIEVIRUS diseases
Abstract

Enterovirus A71 (EV-A71) and coxsackievirus A6 (CVA6) primarily cause hand, foot and mouth disease and have emerged to cause potential fatal neurological and systemic manifestations. However, limited surveillance data collected through passive surveillance systems hampers characterization of their epidemiological dynamics. We fit a series of catalytic models to age-stratified seroprevalence data for EV-A71 and CVA6 collected in England at three time points (2006, 2011 and 2017) to estimate the force of infection (FOI) over time and assess possible changes in transmission. For both serotypes, model comparison does not support the occurrence of important changes in transmission over the study period, and we find that a declining risk of infection with age and / or seroreversion are needed to explain the seroprevalence data. Furthermore, we provide evidence that the increased number of reports of CVA6 during 2006–2017 is unlikely to be explained by changes in surveillance. Therefore, we hypothesize that the increased number of CVA6 cases observed since 2011 must be explained by increased virus pathogenicity. Further studies of seroprevalence data from other countries would allow to confirm this. Our results underscore the value of seroprevalence data to unravel changes in the circulation dynamics of pathogens with weak surveillance systems and large number of asymptomatic infections. Author summary: Enteroviruses commonly cause infections in people of all ages with symptoms ranging from mild to severe. Enterovirus infections create a significant healthcare burden during outbreaks and large epidemics. However, the absence of consistent and systematic surveillance greatly impedes documentation of their true prevalence and collective impact on human health. In the UK, reporting from clinical settings is voluntary and passive, which limits accurate estimation of the overall infection incidence in the population. Here, we use data from seroprevalence surveys, which can detect past infections, to estimate the force of infection (rate at which susceptible individuals acquire infection) of enterovirus A71 and coxsackievirus A6 in England, UK, between 2006 and 2017. We found that transmission intensity for both enterovirus serotypes has remained relatively unchanged in this 12-year period. Furthermore, we analyze changes in serotype-specific enterovirus detections in England over the same period and found evidence that the increased number of reported CVA6 detections cannot only be related to changes in testing intensity. We therefore conclude that the increase in CVA6-related disease cases across England during this period could be attributed to the acquisition of increased pathogenicity (probability of disease after infection) of this serotype. Our approach may be useful to study the population-wide infection burden of other enterovirus serotypes for which clinical surveillance is limited. [ABSTRACT FROM AUTHOR]

Published
2024
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7. Reassessing Reported Deaths and Estimated Infection Attack Rate during the First 6 Months of the COVID-19 Epidemic, Delhi, India

Author

Pons-Salort, Margarita, John, Jacob, Watson, Oliver J., Brazeau, Nicholas F., Verity, Robert, Kang, Gagandeep, and Grassly, Nicholas C.

Subjects
Delhi, India (City) -- Health aspects, Epidemics -- Statistics -- India, Health
Abstract

India had just under 150,000 reported coronavirus disease (COVID-19) deaths in 2020, fewer per 1 million persons than many other countries, such as Spain, France, the United Kingdom, and the [...]

Published
2022
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8. Risk factors for the spread of vaccine-derived type 2 polioviruses after global withdrawal of trivalent oral poliovirus vaccine and the effects of outbreak responses with monovalent vaccine: a retrospective analysis of surveillance data for 51 countries in Africa

Author

Cooper, Laura V, Bandyopadhyay, Ananda S, Gumede, Nicksy, Mach, Ondrej, Mkanda, Pascal, Ndoutabé, Modjirom, Okiror, Samuel O, Ramirez-Gonzalez, Alejandro, Touray, Kebba, Wanyoike, Sarah, Grassly, Nicholas C, and Blake, Isobel M

Published
2022
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9. Estimating the health impact of vaccination against ten pathogens in 98 low-income and middle-income countries from 2000 to 2030: a modelling study

Author

Li, Xiang, Mukandavire, Christinah, Cucunubá, Zulma M, Echeverria Londono, Susy, Abbas, Kaja, Clapham, Hannah E, Jit, Mark, Johnson, Hope L, Papadopoulos, Timos, Vynnycky, Emilia, Brisson, Marc, Carter, Emily D, Clark, Andrew, de Villiers, Margaret J, Eilertson, Kirsten, Ferrari, Matthew J, Gamkrelidze, Ivane, Gaythorpe, Katy A M, Grassly, Nicholas C, Hallett, Timothy B, Hinsley, Wes, Jackson, Michael L, Jean, Kévin, Karachaliou, Andromachi, Klepac, Petra, Lessler, Justin, Li, Xi, Moore, Sean M, Nayagam, Shevanthi, Nguyen, Duy Manh, Razavi, Homie, Razavi-Shearer, Devin, Resch, Stephen, Sanderson, Colin, Sweet, Steven, Sy, Stephen, Tam, Yvonne, Tanvir, Hira, Tran, Quan Minh, Trotter, Caroline L, Truelove, Shaun, van Zandvoort, Kevin, Verguet, Stéphane, Walker, Neff, Winter, Amy, Woodruff, Kim, Ferguson, Neil M, and Garske, Tini

Published
2021
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10. Environmental surveillance for Salmonella Typhi in rivers and wastewater from an informal sewage network in Blantyre, Malawi.

Author

Uzzell, Christopher B., Gray, Elizabeth, Rigby, Jonathan, Troman, Catherine M., Diness, Yohane, Mkwanda, Charity, Tonthola, Katalina, Kanjerwa, Oscar, Salifu, Chifundo, Nyirenda, Tonney, Chilupsya, Chisomo, Msefula, Chisomo, Elviss, Nicola, Grassly, Nicholas C., and Feasey, Nicholas A.

Subjects
SALMONELLA typhi, PUBLIC health, MIXED-use developments, RIVER channels, WATERSHEDS, TYPHOID fever
Abstract

Environmental surveillance for Salmonella Typhi may provide information on the community-level dynamics of typhoid fever in resource poor regions experiencing high disease burden. Many knowledge gaps concerning the feasibility of ES remain, especially in areas lacking formal sewage systems. We implemented protocols for S. Typhi ES, including site selection and catchment population estimation, sample concentration and testing using qPCR for S. Typhi specific gene targets. Between May 2021 and May 2022, we collected grab samples and Moore swabs from 43 sites in Blantyre, Malawi. Catchment characteristics, water quality, and human faecal contamination (qPCR for Bacteroides HF183) were also recorded. Their association with S. Typhi detection was investigated using a logistic mixed-effects regression analysis. Prevalence of S. Typhi in ES samples was 2.1% (1.1–4.0%) and 3.9% (1.9–7.9%) for grab and Moore swab samples, respectively. HF183 was associated S. Typhi positivity, with a unit increase in log genome copies/microlitre increasing the odds of detection of S. Typhi by 1.56 (95% CI: 1.29–1.89) and 1.33 (1.10–1.61) in Moore swabs and grab samples, respectively. The location and timing of S. Typhi detection through ES was not associated with the incidence of typhoid fever reported in associated catchment populations. During this period of relatively low typhoid fever incidence, wastewater surveillance continued to detect S. Typhi in human sewage and wastewater suggesting that ES using natural river systems can be a sensitive indicator of transmission. Author summary: Typhoid fever is a major public health concern throughout many low- and middle-income countries, resulting in significant morbidity and mortality. In recent years, two typhoid-conjugate vaccines have been pre-qualified, with the World Health Organization recommending their targeted use in high incidence, endemic regions. However, quality assured information on the spatio-temporal distribution of typhoid fever is lacking, and scale-up of typhoid vaccination is progressing slowly. Environmental surveillance for Salmonella Typhi in sewage and wastewater may be a cost-effective and scalable approach to identify high-burden regions, thereby motivating vaccine introduction. However, many knowledge gaps regarding the use of environmental surveillance for Salmonella Typhi remain, particularly where human wastewater is unmanaged and its disposal reliant on informal drainage channels and natural river systems. Therefore, we conducted a study in Malawi, Blantyre to ascertain the feasibility of environmental surveillance throughout an urban, natural freshwater river system. We measured S. Typhi prevalence in wastewater contaminated rivers and ditches serving a mixed land use environment with diverse population densities. Whilst detection rates of S. Typhi were relatively low, and no obvious spatial pattern of distribution was observed, this study demonstrates that the presence of S. Typhi throughout the year. It suggests that wastewater testing for S. Typhi may offer a sensitive surveillance tool that complements clinical case reporting and may help identify areas to be prioritized for vaccination rollout. [ABSTRACT FROM AUTHOR]

Published
2024
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11. Comparison of molecular testing strategies for COVID-19 control: a mathematical modelling study

Author

Ainslie, Kylie, Baguelin, Marc, Bhatt, Samir, Boonyasiri, Adhiratha, Brazeau, Nick, Cattarino, Lorenzo, Coupland, Helen, Cucunuba, Zulma, Cuomo-Dannenburg, Gina, Dighe, Amy, Donnelly, Christl, van Elsland, Sabine L, FitzJohn, Richard, Flaxman, Seth, Fraser, Keith, Gaythorpe, Katy, Green, Will, Hamlet, Arran, Hinsley, Wes, Imai, Natsuko, Knock, Edward, Laydon, Daniel, Mellan, Thomas, Mishra, Swapnil, Nedjati-Gilani, Gemma, Nouvellet, Pierre, Okell, Lucy, Ragonnet-Cronin, Manon, Thompson, Hayley A, Unwin, H. Juliette T, Vollmer, Michaela, Volz, Erik, Walters, Caroline, Wang, Yuanrong, Watson, Oliver J, Whittaker, Charles, Whittles, Lilith, Xi, Xiaoyue, Grassly, Nicholas C, Pons-Salort, Margarita, Parker, Edward P K, White, Peter J, and Ferguson, Neil M

Published
2020
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15. Impact of maternal antibodies and microbiota development on the immunogenicity of oral rotavirus vaccine in African, Indian, and European infants

Author

Parker, Edward P. K., Bronowski, Christina, Sindhu, Kulandaipalayam Natarajan C., Babji, Sudhir, Benny, Blossom, Carmona-Vicente, Noelia, Chasweka, Nedson, Chinyama, End, Cunliffe, Nigel A., Dube, Queen, Giri, Sidhartha, Grassly, Nicholas C., Gunasekaran, Annai, Howarth, Deborah, Immanuel, Sushil, Jere, Khuzwayo C., Kampmann, Beate, Lowe, Jenna, Mandolo, Jonathan, Praharaj, Ira, Rani, Bakthavatsalam Sandya, Silas, Sophia, Srinivasan, Vivek Kumar, Turner, Mark, Venugopal, Srinivasan, Verghese, Valsan Philip, Darby, Alistair C., Kang, Gagandeep, and Iturriza-Gómara, Miren

Published
2021
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18. Automated detection and classification of polioviruses from nanopore sequencing reads using piranha

Author

O’Toole, Áine, primary, Colquhoun, Rachel, additional, Ansley, Corey, additional, Troman, Catherine, additional, Maloney, Daniel, additional, Vance, Zoe, additional, Akello, Joyce, additional, Bujaki, Erika, additional, Majumdar, Manasi, additional, Khurshid, Adnan, additional, Arshad, Yasir, additional, Alam, Muhammad Masroor, additional, Martin, Javier, additional, Shaw, Alexander G, additional, Grassly, Nicholas C, additional, and Rambaut, Andrew, additional

Published
2024
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24. The Duration of Intestinal Immunity After an Inactivated Poliovirus Vaccine Booster Dose in Children Immunized With Oral Vaccine: A Randomized Controlled Trial

Author

John, Jacob, Giri, Sidhartha, Karthikeyan, Arun S., Lata, Dipti, Jeyapaul, Shalini, Rajan, Anand K., Kumar, Nirmal, Dhanapal, Pavithra, Venkatesan, Jayalakshmi, Mani, Mohanraj, Hanusha, Janardhanan, Raman, Uma, Moses, Prabhakar D., Abraham, Asha, Bahl, Sunil, Bandyopadhyay, Ananda S., Ahmad, Mohammad, Grassly, Nicholas C., and Kang, Gagandeep

Published
2017

25. Environmental surveillance for Salmonella Typhi and its association with typhoid fever incidence in India and Malawi

Author

Uzzell, Christopher B, primary, Abraham, Dilip, additional, Rigby, Jonathan, additional, Troman, Catherine M, additional, Nair, Satheesh, additional, Elviss, Nicola, additional, Kathiresan, Lalithambigai, additional, Srinivasan, Rajan, additional, Balaji, Veeraraghavan, additional, Zhou, Nicolette A, additional, Meschke, John Scott, additional, John, Jacob, additional, Kang, Gagandeep, additional, Feasey, Nicholas, additional, Mohan, Venkata Raghava, additional, and Grassly, Nicholas C, additional

Published
2023
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26. Automated detection and classification of polioviruses from nanopore sequencing reads using piranha

Author

O'Toole, Aine N, primary, Colquhoun, Rachel, additional, Ansley, Corwin, additional, Troman, Catherine, additional, Maloney, Daniel, additional, Vance, Zoe, additional, Akello, Joyce, additional, Bujaki, Erika, additional, Majumdar, Manasi, additional, Khurshid, Adnan, additional, Arshad, Yasir, additional, Alam, Muhammad Masroor, additional, Martin, Javier, additional, Shaw, Alexander G, additional, and Grassly, Nicholas C, additional

Published
2023
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27. Study design and baseline results of an open-label cluster randomized community-intervention trial to assess the effectiveness of a modified mass deworming program in reducing hookworm infection in a tribal population in southern India

Author

Sarkar, Rajiv, Rose, Anuradha, Mohan, Venkata R., Ajjampur, Sitara S.R., Veluswamy, Vasanthakumar, Srinivasan, Rajan, Muliyil, Jayaprakash, Rajshekhar, Vedantam, George, Kuryan, Balraj, Vinohar, Grassly, Nicholas C., Anderson, Roy M., Brooker, Simon J., and Kang, Gagandeep

Published
2017
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29. Environmental Surveillance for Salmonella Typhi and its Association With Typhoid Fever Incidence in India and Malawi.

Author

Uzzell, Christopher B, Abraham, Dilip, Rigby, Jonathan, Troman, Catherine M, Nair, Satheesh, Elviss, Nicola, Kathiresan, Lalithambigai, Srinivasan, Rajan, Balaji, Veeraraghavan, Zhou, Nicolette A, Meschke, John Scott, John, Jacob, Kang, Gagandeep, Feasey, Nicholas, Mohan, Venkata Raghava, and Grassly, Nicholas C

Subjects
SALMONELLA typhi, TYPHOID fever, FECAL contamination, PUBLIC utilities, GENE targeting, PUBLIC health
Abstract

Background Environmental surveillance (ES) for Salmonella Typhi potentially offers a low-cost tool to identify communities with a high burden of typhoid fever. Methods We developed standardized protocols for typhoid ES, including sampling site selection, validation, characterization; grab or trap sample collection, concentration; and quantitative PCR targeting Salmonella genes (ttr , staG, and tviB) and a marker of human fecal contamination (HF183). ES was implemented over 12 months in a historically high typhoid fever incidence setting (Vellore, India) and a lower incidence setting (Blantyre, Malawi) during 2021–2022. Results S. Typhi prevalence in ES samples was higher in Vellore compared with Blantyre; 39/520 (7.5%; 95% confidence interval [CI], 4.4%–12.4%) vs 11/533 (2.1%; 95% CI, 1.1%–4.0%) in grab and 79/517 (15.3%; 95% CI, 9.8%–23.0%) vs 23/594 (3.9%; 95% CI, 1.9%–7.9%) in trap samples. Detection was clustered by ES site and correlated with site catchment population in Vellore but not Blantyre. Incidence of culture-confirmed typhoid in local hospitals was low during the study and zero some months in Vellore despite S. Typhi detection in ES. Conclusions ES describes the prevalence and distribution of S. Typhi even in the absence of typhoid cases and could inform vaccine introduction. Expanded implementation and comparison with clinical and serological surveillance will further establish its public health utility. [ABSTRACT FROM AUTHOR]

Published
2024
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30. The effect of azithromycin on the immunogenicity of oral poliovirus vaccine: a double-blind randomised placebo-controlled trial in seronegative Indian infants

Author

Grassly, Nicholas C, Praharaj, Ira, Babji, Sudhir, Kaliappan, Saravanakumar Puthupalayam, Giri, Sidhartha, Venugopal, Srinivasan, Parker, Edward P K, Abraham, Asha, Muliyil, Jayaprakash, Doss, Sridhar, Raman, Uma, Liu, Jie, Peter, John Victor, Paranjape, Meghana, Jeyapaul, Shalini, Balakumar, Shailaja, Ravikumar, Jeniffer, Srinivasan, Rajan, Bahl, Sunil, Iturriza-Gómara, Miren, Uhlig, Holm H, Houpt, Eric R, John, Jacob, and Kang, Gagandeep

Published
2016
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32. Burden of Typhoid and Paratyphoid Fever in India

Author

John, Jacob, primary, Bavdekar, Ashish, additional, Rongsen-Chandola, Temsunaro, additional, Dutta, Shanta, additional, Gupta, Madhu, additional, Kanungo, Suman, additional, Sinha, Bireshwar, additional, Srinivasan, Manikandan, additional, Shrivastava, Ankita, additional, Bansal, Adarsh, additional, Singh, Ashita, additional, Koshy, Roshine M., additional, Jinka, Dasharatha R., additional, Thomas, Mathew S., additional, Alexander, Anna P., additional, Thankaraj, Shajin, additional, Ebenezer, Sheena E., additional, Karthikeyan, Arun S., additional, Kumar, Dilesh, additional, Njarekkattuvalappil, Swathi K., additional, Raju, Reshma, additional, Sahai, Nikhil, additional, Veeraraghavan, Balaji, additional, Murhekar, Manoj V., additional, Mohan, Venkata R., additional, Natarajan, Sindhu K., additional, Ramanujam, Karthikeyan, additional, Samuel, Prasanna, additional, Lo, Nathan C., additional, Andrews, Jason, additional, Grassly, Nicholas C., additional, and Kang, Gagandeep, additional

Published
2023
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33. Comparison of Eleven RNA Extraction Methods for Poliovirus Direct Molecular Detection in Stool Samples

Author

Akello, Joyce Odeke, primary, Bujaki, Erika, additional, Shaw, Alexander G., additional, Khurshid, Adnan, additional, Arshad, Yasir, additional, Troman, Catherine, additional, Majumdar, Manasi, additional, O'Toole, Áine, additional, Rambaut, Andrew, additional, Alam, Muhammad Masroor, additional, Martin, Javier, additional, and Grassly, Nicholas C., additional

Published
2023
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35. Modelling the spread of serotype-2 vaccine derived-poliovirus outbreak in Pakistan and Afghanistan to inform outbreak control strategies in the context of the COVID-19 pandemic

Author

Molodecky, Natalia A, primary, Jafari, Hamid, additional, Safdar, Rana M, additional, Ahmed, Jamal A, additional, Mahamud, Abdirahman, additional, Bandyopadhyay, Ananda S, additional, Shukla, Hemant, additional, Quddus, Arshad, additional, Zaffran, Michel, additional, Sutter, Roland W, additional, Grassly, Nicholas C, additional, and Blake, Isobel M, additional

Published
2023
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38. Effect of maternal immunisation with multivalent vaccines containing inactivated poliovirus vaccine (IPV) on infant IPV immune response: A phase 4, multi-centre randomised trial

Author

Grassly, Nicholas C, primary, Andrews, Nick, additional, Cooper, Gillian, additional, Stephens, Laura, additional, Waight, Pauline, additional, Jones, Christine E, additional, Heath, Paul T, additional, Calvert, Anna, additional, Southern, Jo, additional, Martin, Javier, additional, and Miller, Elizabeth, additional

Published
2023
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39. Estimated effect of inactivated poliovirus vaccine campaigns, Nigeria and Pakistan, January 2014-April 2016

Author

Shirreff, George, Wadood, Mufti Zubair, Vaz, Rui Gama, Sutter, Roland W., and Grassly, Nicholas C.

Subjects
Viral vaccines -- Comparative analysis, Poliomyelitis -- Prevention, Health
Abstract

The live attenuated oral poliovirus vaccine (OPV) is cheap and easy to administer; therefore, it has been the vaccine of choice for the Global Polio Eradication Initiative. However, the immunogenicity [...]

Published
2017
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42. Environmental surveillance for Salmonella Typhi as a tool to estimate the incidence of typhoid fever in low-income populations.

Author

Uzzell, Christopher B., primary, Troman, Catherine M., additional, Rigby, Jonathan, additional, Raghava Mohan, Venkata, additional, John, Jacob, additional, Abraham, Dilip, additional, Srinivasan, Rajan, additional, Nair, Satheesh, additional, Meschke, John Scott, additional, Elviss, Nicola, additional, Kang, Gagandeep, additional, Feasey, Nicholas A., additional, and Grassly, Nicholas C., additional

Published
2023
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44. Modelling Trachoma for Control Programmes

Author

Gambhir, Manoj, Basáñez, María-Gloria, Blake, Isobel M., Grassly, Nicholas C., Back, Nathan, editor, Cohen, Irun R., editor, Lajtha, Abel, editor, Lambris, John D., editor, Paoletti, Rodolfo, editor, Michael, Edwin, editor, and Spear, Robert C., editor

Published
2010
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48. Efficacy of inactivated poliovirus vaccine in India

Author

Jafari, Hamid, Deshpande, Jagadish M., Sutter, Roland W., Bahl, Sunil, Verma, Harish, Ahmad, Mohammad, Kunwar, Abhishek, Vishwakarma, Rakesh, Agarwal, Ashutosh, Jain, Shilpi, Estivariz, Concepcion, Sethi, Raman, Molodecky, Natalie A., Grassly, Nicholas C., Pallansch, Mark A., Chatterjee, Arani, and Aylward, R. Bruce

Published
2014

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