Project description:Genomic epidemiology of Neisseria gonorrhoeae to investigate the distribution of gonococcal lineages in all five main macroregions of Brazil, 2015-2016
Project description:During 2015-2016, Cape Verde, an island nation off the coast of West Africa, experienced a Zika virus (ZIKV) outbreak involving 7,580 suspected Zika cases and 18 microcephaly cases. Analysis of the complete genomes of 3 ZIKV isolates from the outbreak indicated the strain was of the Asian (not African) lineage. The Cape Verde ZIKV sequences formed a distinct monophylogenetic group and possessed 1-2 (T659A, I756V) unique amino acid changes in the envelope protein. Phylogeographic and serologic evidence support earlier introduction of this lineage into Cape Verde, possibly from northeast Brazil, between June 2014 and August 2015, suggesting cryptic circulation of the virus before the initial wave of cases were detected in October 2015. These findings underscore the utility of genomic-scale epidemiology for outbreak investigations.
Project description:BACKGROUND:India has launched the malaria elimination initiative in February 2016. Studies suggest that estimates of malaria are useful to rationalize interventions and track their impact. Hence, a national study was launched to estimate burden of malaria in India in 2015. METHODS:For sampling, all 624 districts of India were grouped in three Annual Parasite Incidence (cases per thousand population) categories, < two (low); two-five (moderate) and > five (high) API. Using probability proportional to size (PPS) method, two districts from each stratum were selected covering randomly 200,000 persons per district. Active surveillance was strengthened with 40 trained workers per study district. Data on malaria cases and deaths was collated from all health care providers i.e. pathological laboratories, private practitioners and hospitals in private and public health sectors and was used for analysis and burden estimation. RESULTS:Out of 1215,114 population under surveillance, 198,612 (16.3%) tests were performed and 19,386 (9.7%) malaria cases were detected. The malaria cases estimated in India were 3875,078 (95% confidence interval 3792,018-3958,137) with API of 3.05 (2.99-3.12) including 2789,483 (2740,577-2838,389) Plasmodium falciparum with Annual Falciparum Incidence of 2.2 (2.16-2.24). Out of 8025 deaths investigated, 102 (1.27%) were attributed to malaria. The estimated deaths in India were 29,341 (23,354-35,327) including 19,067 (13,665-24,470) confirmed and 10,274 (7694-12,853) suspected deaths in 2015-2016. CONCLUSIONS:Estimated malaria incidence was about four folds greater than one million reported by the national programme, but three folds lesser than thirteen million estimated by the World Health Organization (WHO). However, the estimated deaths were 93 folds more than average 313 deaths reported by the national malaria programme in 2015-2016. The 29,341 deaths were comparable with 24,000 deaths in 2015 and 22,786 deaths in 2016 estimated by the WHO for India. These malaria estimates can serve as a benchmark for tracking the success of malaria elimination campaign in India.
Project description:ObjectiveHuman astroviruses (HAstVs) are single-stranded RNA viruses of the Astroviridae family. Infection of classic HAstVs is one of the most common causes of acute viral gastroenteritis (infectious viral diarrhea). There is a lack of data on the prevalence and genetic characterization of classic HAstVs in acute viral gastroenteritis in the whole population. This study aimed to investigate the epidemiological trend, genotypes, viral co-infections, and viral loads of classic HAstVs in Shanghai, China, from January 2015 to December 2016.MethodsA total of 6,051 non-redundant stool samples were collected in outpatients with acute diarrhea in Shanghai from January 2015 to December 2016. One-step real-time RT-PCR was used for screening viral diarrhea, including rotavirus A, rotavirus B, rotavirus C, norovirus genotype I and II, classic human astroviruses, and sapovirus. Real-time PCR was used for screening human enteric adenoviruses. Conventional RT-PCR was used for the amplification of viral fragments for genotyping. PCR products were sequenced and used for the construction of phylogenetic trees.ResultsThe detection rate of classic HAstVs was 1.55% (94/6,051). The prevalence of HAstV infection displayed a typical winter/spring (December to March) seasonality and was highest in the 5-14 age group. Eighty-six samples were genotyped, which revealed HAstV-1 as the most prevalent genotype, followed by HAstV-5, HAstV-4, HAstV- 2, HAstV-8, and HAstV-3. There was a dramatic rise in the prevalence of HAstV-4 from December 2015 to March 2016, and the viral loads of HAstV-4 were significantly higher than those of other genotypes. Among the mixed infection samples, noroviruses were found to be the most frequently co-infected enteric viruses with HAstV.ConclusionMultiple genotypes of classic HAstVs circulated in Shanghai from January 2015 to December 2016. For the first time, HAstV-3\4\5\8 were detected in Shanghai.
Project description:Echovirus 18 (E18), a serotype of Enterovirus B (EV-B) species, is an important pathogen in aseptic meningitis. E18 had rarely been detected in mainland China, but became the predominant pathogen associated with viral encephalitis (VE) and meningitis in Hebei province for the first time in 2015. To investigate the molecular epidemiology and genetic characteristics of E18 in mainland China, sixteen E18 strains from patient throat swabs with hand, foot, and mouth disease (HFMD) in six provinces in China collected between 2015 and 2016, and four E18 strains isolated from 18 patient cerebrospinal fluid specimens with VE in Hebei Province in 2015 were obtained and sequenced. Combined with the sequences from the GenBank database, we performed an extensive genetic analysis. Phylogenetic analysis of VP1 gene sequences revealed that all E18 strains from mainland China after 2015 belonged to subgenotype C2. There were no obvious specific differences in phylogenetic and variation analyses of E18 genome sequences between HFMD and VE/meningitis strains. Potential multiple recombination may have occurred in the 5'-untranslated region and in the P2 and P3 nonstructural protein-encoding regions of E18 strains from China. The current E18 strains were potential multiple-recombinant viruses. Overall, these findings supported that E18 caused HFMD, VE, and meningitis, although there were no significant associations between clinical features and viral genomic characteristics.