Last data update: Jun 24, 2024. (Total: 47078 publications since 2009)
Records 1-9 (of 9 Records) |
Query Trace: Tessema Z [original query] |
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XBB.1, BQ1.1 and atypical BA.4.6/XBB.1 recombinants predominate current SARS-CoV-2 Wavelets with flu-like symptoms in Cameroon: A snapshot from genomic surveillance
Fokam J , Ngoufack Jagni Semengue E , Gouissi Anguechia DH , Etame NK , Takou D , Mandeng N , Kengni Ngueko MA , Beloumou Angong G , Djupsa Ndjeyep S , Chenwi Ambe C , Nka AD , Molimbou E , Mundo Nayang AR , Moko Fotso LG , Tambe Ayuk Ngwese D , Tueguem PP , Tommo Tchouaket CM , Ka'e AC , Fainguem N , Abega Abega C , Halle-Ekane EG , Esso L , Etoundi Mballa AG , Shang J , Ndongmo CB , Cappelli G , Kifle Tessema S , ZKBissek AC , Colizzi V , Ndjolo A , Perno CF , Ndembi N . PLOS Glob Public Health 2024 4 (5) e0003153 As of December 2022, Cameroon had observed a slight resurgence of COVID-19, raising concerns on genomic surveillance of related-SARS-CoV-2 variants under circulation. Following a laboratory-based survey, positive SARS-CoV-2 samples detected from December-2022 through March-2023 were processed for targeted sequencing at the Chantal BIYA International Reference Centre (CIRCB) in Yaoundé-Cameroon. From all positive cases detected, 13 were successfully sequenced (mean age 34 years, 70% female); the majority of the cases were unvaccinated (70%, 9/13) and symptomatic (92%, 12/13); all with flu-like symptoms (100%, 12/12). Following RT-PCR, the median cycle threshold was 22.23 [18-24] for the N gene; and 24.09 [20-26] for the ORF gene, underscoring high viral loads. Phylogenetic analysis of nucleotide sequences identified four major sub-variants in circulation, of which BA.5 (3/13), the recombinants BQ.1.1 (4/13), XBB.1 (4/13) and novel atypical variant of BA.4.6/XBB.1 (2/13). This snapshot surveillance indicates the introduction/emergence and circulation of new Omicron sub-variants, all accompanied by minor/mild symptoms. However, these new sub-variants and recombinants call for continuous genomic surveillance to prevent further resurgence of Covid-19 epidemiological wave. |
An updated framework for SARS-CoV-2 variants reflects the unpredictability of viral evolution
Subissi L , Otieno JR , Worp N , Attar Cohen H , Oude Munnink BB , Abu-Raddad LJ , Alm E , Barakat A , Barclay WS , Bhiman JN , Caly L , Chand M , Chen M , Cullinane A , de Oliveira T , Drosten C , Druce J , Effler P , El Masry I , Faye A , Ghedin E , Grant R , Haagmans BL , Happi C , Herring BL , Hodcroft EB , Ikejezie J , Katawera V , Kassamali ZA , Leo YS , Leung GM , Kondor RJ , Marklewitz M , Mendez-Rico J , Melhem NM , Munster V , Nahapetyan K , Naindoo D , Oh DY , Peacock TP , Peiris M , Peng Z , Poon LLM , Rambaut A , Saha S , Shen Y , Siqueira MM , Volz E , Tessema SK , Thiel V , Triki H , van der Werf S , von Eije K , Cunningham J , Koopmans MPG , von Gottberg A , Agrawal A , Van Kerkhove MD . Nat Med 2024 |
A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis.
Miotto P , Tessema B , Tagliani E , Chindelevitch L , Starks AM , Emerson C , Hanna D , Kim PS , Liwski R , Zignol M , Gilpin C , Niemann S , Denkinger CM , Fleming J , Warren RM , Crook D , Posey J , Gagneux S , Hoffner S , Rodrigues C , Comas I , Engelthaler DM , Murray M , Alland D , Rigouts L , Lange C , Dheda K , Hasan R , Ranganathan UDK , McNerney R , Ezewudo M , Cirillo DM , Schito M , Köser CU , Rodwell TC . Eur Respir J 2017 50 (6) A clear understanding of the genetic basis of antibiotic resistance in Mycobacterium tuberculosis is required to accelerate the development of rapid drug susceptibility testing methods based on genetic sequence.Raw genotype-phenotype correlation data were extracted as part of a comprehensive systematic review to develop a standardised analytical approach for interpreting resistance associated mutations for rifampicin, isoniazid, ofloxacin/levofloxacin, moxifloxacin, amikacin, kanamycin, capreomycin, streptomycin, ethionamide/prothionamide and pyrazinamide. Mutation frequencies in resistant and susceptible isolates were calculated, together with novel statistical measures to classify mutations as high, moderate, minimal or indeterminate confidence for predicting resistance.We identified 286 confidence-graded mutations associated with resistance. Compared to phenotypic methods, sensitivity (95% CI) for rifampicin was 90.3% (89.6-90.9%), while for isoniazid it was 78.2% (77.4-79.0%) and their specificities were 96.3% (95.7-96.8%) and 94.4% (93.1-95.5%), respectively. For second-line drugs, sensitivity varied from 67.4% (64.1-70.6%) for capreomycin to 88.2% (85.1-90.9%) for moxifloxacin, with specificity ranging from 90.0% (87.1-92.5%) for moxifloxacin to 99.5% (99.0-99.8%) for amikacin.This study provides a standardised and comprehensive approach for the interpretation of mutations as predictors of M. tuberculosis drug-resistant phenotypes. These data have implications for the clinical interpretation of molecular diagnostics and next-generation sequencing as well as efficient individualised therapy for patients with drug-resistant tuberculosis. |
Targeted and whole-genome sequencing reveal a north-south divide in P. falciparum drug resistance markers and genetic structure in Mozambique
da Silva C , Boene S , Datta D , Rovira-Vallbona E , Aranda-Díaz A , Cisteró P , Hathaway N , Tessema S , Chidimatembue A , Matambisso G , Nhama A , Macete E , Pujol A , Nhamussua L , Galatas B , Guinovart C , Enosse S , De Carvalho E , Rogier E , Plucinski MM , Colborn J , Zulliger R , Saifodine A , Alonso PL , Candrinho B , Greenhouse B , Aide P , Saute F , Mayor A . Commun Biol 2023 6 (1) 619 Mozambique is one of the four African countries which account for over half of all malaria deaths worldwide, yet little is known about the parasite genetic structure in that country. We performed P. falciparum amplicon and whole genome sequencing on 2251 malaria-infected blood samples collected in 2015 and 2018 in seven provinces of Mozambique to genotype antimalarial resistance markers and interrogate parasite population structure using genome-wide microhaplotyes. Here we show that the only resistance-associated markers observed at frequencies above 5% were pfmdr1-184F (59%), pfdhfr-51I/59 R/108 N (99%) and pfdhps-437G/540E (89%). The frequency of pfdhfr/pfdhps quintuple mutants associated with sulfadoxine-pyrimethamine resistance increased from 80% in 2015 to 89% in 2018 (p < 0.001), with a lower expected heterozygosity and higher relatedness of microhaplotypes surrounding pfdhps mutants than wild-type parasites suggestive of recent selection. pfdhfr/pfdhps quintuple mutants also increased from 72% in the north to 95% in the south (2018; p < 0.001). This resistance gradient was accompanied by a concentration of mutations at pfdhps-436 (17%) in the north, a south-to-north increase in the genetic complexity of P. falciparum infections (p = 0.001) and a microhaplotype signature of regional differentiation. The parasite population structure identified here offers insights to guide antimalarial interventions and epidemiological surveys. |
An early warning system for emerging SARS-CoV-2 variants.
Subissi L , von Gottberg A , Thukral L , Worp N , Oude Munnink BB , Rathore S , Abu-Raddad LJ , Aguilera X , Alm E , Archer BN , Attar Cohen H , Barakat A , Barclay WS , Bhiman JN , Caly L , Chand M , Chen M , Cullinane A , de Oliveira T , Drosten C , Druce J , Effler P , El Masry I , Faye A , Gaseitsiwe S , Ghedin E , Grant R , Haagmans BL , Herring BL , Iyer SS , Kassamali Z , Kakkar M , Kondor RJ , Leite JA , Leo YS , Leung GM , Marklewitz M , Moyo S , Mendez-Rico J , Melhem NM , Munster V , Nahapetyan K , Oh DY , Pavlin BI , Peacock TP , Peiris M , Peng Z , Poon LLM , Rambaut A , Sacks J , Shen Y , Siqueira MM , Tessema SK , Volz EM , Thiel V , van der Werf S , Briand S , Perkins MD , Van Kerkhove MD , Koopmans MPG , Agrawal A . Nat Med 2022 28 (6) 1110-1115 Global sequencing and surveillance capacity for SARS-CoV-2 must be strengthened and combined with multidisciplinary studies of infectivity, virulence and immune escape, in order to track the unpredictable evolution of the ongoing COVID-19 pandemic. | | In June 2020, the World Health Organization (WHO) SARS-CoV-2 evolution working group was established to track SARS-CoV-2 variants and their specific genetic changes and to monitor viral characteristics and their impact on medical and non-medical countermeasures, including vaccines against COVID-19. In November 2021, this working group transitioned to a formal WHO Technical Advisory Group on Virus Evolution (TAG-VE), with the aim of developing and implementing a global risk-monitoring framework for SARS-CoV-2 variants, based on a multidisciplinary approach that includes in silico, virological, clinical and epidemiological data. |
Innovations in public health surveillance: updates from a forum convened by the WHO Hub for Pandemic and Epidemic Intelligence, 2 and 3 February 2022.
Morgan Oliver , Redies Isabel , Beatriz Leiva Rioja Zoila , Brownstein John , George Dylan , Golding Josie , Hanefeld Johanna , Horby Peter , Lee Christopher , Mikhailov Danil , Philip Wolfgang , Scarpino Samuel , Kifle Tessema Sofonias , Ihekweazu Chikwe . Euro Surveill 2022 27 (15) In the 2 years since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) there has been an unprecedented collective effort from the academic, public, and private sectors to advance surveillance for pandemic preparedness and response. The coronavirus disease (COVID-19) pandemic has created momentum that will define the future of public health intelligence. On 2 and 3 February 2022, the World Health Organization (WHO) Hub for Pandemic and Epidemic Intelligence convened a meeting of a small group of surveillance innovators to share insights and approaches about their initiatives and future directions. The meeting served as an opportunity for participants to share updates about their work, to explore potential for collaboration, exchange ideas, cross-fertilise our work and discuss challenges in the field of surveillance. Although the group of attendees was not geographically representative of the global surveillance community, the meeting was the first in a planned series of exchanges convened by the WHO Pandemic Hub that will generate dialogue among global thought leaders and new voices in the surveillance community. In this first convening we discussed several themes, including what is meaningful collaboration for success; how to bring the public back into public health; what are individual-centred approaches; how new kinds of data have new privacy concerns; how government structures affect the functioning of surveillance systems; how to inform the decisionmaking process; cross-scaling and down-scaling tools and technologies; investing in human talent and future practitioners; and achieving sustainability into surveillance. In this meeting report, we summarise the discussions on innovations in public health surveillance and provide a list with references and links to the organisations and initiatives represented at the meeting. |
Geospatial transmission hotspots of recent HIV infection - Malawi, October 2019-March 2020
Telford CT , Tessema Z , Msukwa M , Arons MM , Theu J , Bangara FF , Ernst A , Welty S , O'Malley G , Dobbs T , Shanmugam V , Kabaghe A , Dale H , Wadonda-Kabondo N , Gugsa S , Kim A , Bello G , Eaton JW , Jahn A , Nyirenda R , Parekh BS , Shiraishi RW , Kim E , Tobias JL , Curran KG , Payne D , Auld AF . MMWR Morb Mortal Wkly Rep 2022 71 (9) 329-334 Persons infected with HIV are more likely to transmit the virus during the early stages (acute and recent) of infection, when viral load is elevated and opportunities to implement risk reduction are limited because persons are typically unaware of their status (1,2). Identifying recent HIV infections (acquired within the preceding 12 months)* is critical to understanding the factors and geographic areas associated with transmission to strengthen program intervention, including treatment and prevention (2). During June 2019, a novel recent infection surveillance initiative was integrated into routine HIV testing services in Malawi, a landlocked country in southeastern Africa with one of the world's highest prevalences of HIV infection.(†) The objectives of this initiative were to collect data on new HIV diagnoses, characterize the epidemic, and guide public health response (2). New HIV diagnoses were classified as recent infections based on a testing algorithm that included results from the rapid test for recent infection (RTRI)(§) and HIV viral load testing (3,4). Among 9,168 persons aged ≥15 years with a new HIV diagnosis who received testing across 103 facilities during October 2019-March 2020, a total of 304 (3.3%) were classified as having a recent infection. Higher proportions of recent infections were detected among females, persons aged <30 years, and clients at maternal and child health and youth clinics. Using a software application that analyzes clustering in spatially referenced data, transmission hotspots were identified with rates of recent infection that were significantly higher than expected. These near real-time HIV surveillance data highlighted locations across Malawi, allowing HIV program stakeholders to assess program gaps and improve access to HIV testing, prevention, and treatment services. Hotspot investigation information could be used to tailor HIV testing, prevention, and treatment to ultimately interrupt transmission. |
Injury-related gaining momentum as external causes of deaths in Ethiopian health and demographic surveillance sites: evidence from verbal autopsy study
Gelaye KA , Tessema F , Tariku B , Abera SF , Gebru AA , Assefa N , Zelalem D , Dedefo M , Kondal M , Kote M , Sisay MM , Mekonnen W , Terefe MW , Biks GA , Eshetu F , Abera M , Fekadu Y , Hailu GB , Tilahun E , Lakew Y . Glob Health Action 2018 11 (1) 1430669 BACKGROUND: In Ethiopia, though all kinds of mortality due to external causes are an important component of overall mortality often not counted or documented on an individual basis. OBJECTIVE: The aim of this study was to describe the patterns of mortality from external causes using verbal autopsy (VA) method at the Ethiopian HDSS Network sites. METHODS: All deaths at Ethiopian HDSS sites were routinely registered and followed up with VA interviews. The VA forms comprised deaths up to 28 days, between four weeks and 14 years and 15 years and above. The cause of a death was ascertained based on an interview with next of families or other caregivers using a standardized questionnaire that draws information on signs, symptoms, medical history and circumstances preceding death after 45 days mourning period. Two physician assigned probable causes of death as underlying, immediate and contributing factors independently using information in VA forms based on the WHO ICD-10 and VA code system. Disagreed cases sent to third physician for independent review and diagnosis. The final cause of death considered when two of the three physicians assigned underlying cause of death; otherwise, labeled as undetermined. RESULTS: In the period from 2009 to 2013, a total of 9719 deaths were registered. Of the total deaths, 623 (6.4%) were from external causes. Of these, accidental drowning and submersion, 136 (21.8%), accidental fall, 113 (18.1%) and transport-related accidents, 112 (18.0%) were the topmost three leading external causes of deaths. About 436 (70.0%) of deaths were from the age group above 15 years old. Drowning and submersion and transport-related accidents were high in age group between 5 and 14 years old. CONCLUSION: In this study, external causes of death are significant public health problems and require attention as one of prior health agenda. |
Global, regional, and national cancer incidence, mortality, years of life lost, years lived with disability, and disability-adjusted life-years for 32 cancer groups, 1990 to 2015: a systematic analysis for the Global Burden of Disease Study
Fitzmaurice C , Allen C , Barber RM , Barregard L , Bhutta ZA , Brenner H , Dicker DJ , Chimed-Orchir O , Dandona R , Dandona L , Fleming T , Forouzanfar MH , Hancock J , Hay RJ , Hunter-Merrill R , Huynh C , Hosgood HD , Johnson CO , Jonas JB , Khubchandani J , Kumar GA , Kutz M , Lan Q , Larson HJ , Liang X , Lim SS , Lopez AD , MacIntyre MF , Marczak L , Marquez N , Mokdad AH , Pinho C , Pourmalek F , Salomon JA , Sanabria JR , Sandar L , Sartorius B , Schwartz SM , Shackelford KA , Shibuya K , Stanaway J , Steiner C , Sun J , Takahashi K , Vollset SE , Vos T , Wagner JA , Wang H , Westerman R , Zeeb H , Zoeckler L , Abd-Allah F , Ahmed MB , Alabed S , Alam NK , Aldhahri SF , Alem G , Alemayohu MA , Ali R , Al-Raddadi R , Amare A , Amoako Y , Artaman A , Asayesh H , Atnafu N , Awasthi A , Saleem HB , Barac A , Bedi N , Bensenor I , Berhane A , Bernabe E , Betsu B , Binagwaho A , Boneya D , Campos-Nonato I , Castaneda-Orjuela C , Catala-Lopez F , Chiang P , Chibueze C , Chitheer A , Choi JY , Cowie B , Damtew S , das Neves J , Dey S , Dharmaratne S , Dhillon P , Ding E , Driscoll T , Ekwueme D , Endries AY , Farvid M , Farzadfar F , Fernandes J , Fischer F , GHiwot TT , Gebru A , Gopalani S , Hailu A , Horino M , Horita N , Husseini A , Huybrechts I , Inoue M , Islami F , Jakovljevic M , James S , Javanbakht M , Jee SH , Kasaeian A , Kedir MS , Khader YS , Khang YH , Kim D , Leigh J , Linn S , Lunevicius R , El Razek HM , Malekzadeh R , Malta DC , Marcenes W , Markos D , Melaku YA , Meles KG , Mendoza W , Mengiste DT , Meretoja TJ , Miller TR , Mohammad KA , Mohammadi A , Mohammed S , Moradi-Lakeh M , Nagel G , Nand D , Le Nguyen Q , Nolte S , Ogbo FA , Oladimeji KE , Oren E , Pa M , Park EK , Pereira DM , Plass D , Qorbani M , Radfar A , Rafay A , Rahman M , Rana SM , Soreide K , Satpathy M , Sawhney M , Sepanlou SG , Shaikh MA , She J , Shiue I , Shore HR , Shrime MG , So S , Soneji S , Stathopoulou V , Stroumpoulis K , Sufiyan MB , Sykes BL , Tabares-Seisdedos R , Tadese F , Tedla BA , Tessema GA , Thakur JS , Tran BX , Ukwaja KN , Uzochukwu BS , Vlassov VV , Weiderpass E , Wubshet Terefe M , Yebyo HG , Yimam HH , Yonemoto N , Younis MZ , Yu C , Zaidi Z , Zaki ME , Zenebe ZM , Murray CJ , Naghavi M . JAMA Oncol 2016 3 (4) 524-548 Importance: Cancer is the second leading cause of death worldwide. Current estimates on the burden of cancer are needed for cancer control planning. Objective: To estimate mortality, incidence, years lived with disability (YLDs), years of life lost (YLLs), and disability-adjusted life-years (DALYs) for 32 cancers in 195 countries and territories from 1990 to 2015. Evidence Review: Cancer mortality was estimated using vital registration system data, cancer registry incidence data (transformed to mortality estimates using separately estimated mortality to incidence [MI] ratios), and verbal autopsy data. Cancer incidence was calculated by dividing mortality estimates through the modeled MI ratios. To calculate cancer prevalence, MI ratios were used to model survival. To calculate YLDs, prevalence estimates were multiplied by disability weights. The YLLs were estimated by multiplying age-specific cancer deaths by the reference life expectancy. DALYs were estimated as the sum of YLDs and YLLs. A sociodemographic index (SDI) was created for each location based on income per capita, educational attainment, and fertility. Countries were categorized by SDI quintiles to summarize results. Findings: In 2015, there were 17.5 million cancer cases worldwide and 8.7 million deaths. Between 2005 and 2015, cancer cases increased by 33%, with population aging contributing 16%, population growth 13%, and changes in age-specific rates contributing 4%. For men, the most common cancer globally was prostate cancer (1.6 million cases). Tracheal, bronchus, and lung cancer was the leading cause of cancer deaths and DALYs in men (1.2 million deaths and 25.9 million DALYs). For women, the most common cancer was breast cancer (2.4 million cases). Breast cancer was also the leading cause of cancer deaths and DALYs for women (523000 deaths and 15.1 million DALYs). Overall, cancer caused 208.3 million DALYs worldwide in 2015 for both sexes combined. Between 2005 and 2015, age-standardized incidence rates for all cancers combined increased in 174 of 195 countries or territories. Age-standardized death rates (ASDRs) for all cancers combined decreased within that timeframe in 140 of 195 countries or territories. Countries with an increase in the ASDR due to all cancers were largely located on the African continent. Of all cancers, deaths between 2005 and 2015 decreased significantly for Hodgkin lymphoma (-6.1% [95% uncertainty interval (UI), -10.6% to -1.3%]). The number of deaths also decreased for esophageal cancer, stomach cancer, and chronic myeloid leukemia, although these results were not statistically significant. Conclusion and Relevance: As part of the epidemiological transition, cancer incidence is expected to increase in the future, further straining limited health care resources. Appropriate allocation of resources for cancer prevention, early diagnosis, and curative and palliative care requires detailed knowledge of the local burden of cancer. The GBD 2015 study results demonstrate that progress is possible in the war against cancer. However, the major findings also highlight an unmet need for cancer prevention efforts, including tobacco control, vaccination, and the promotion of physical activity and a healthy diet. |
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