Phylogenetic studies demonstrated that outbreak strains belonged to the East-Central African lineage.
Our data confirm that influenza is prevalent in Senegal, occurs in seasonal epidemics, and contributes to the burden of respiratory diseases in all age groups.
BackgroundEnteroviruses are common human pathogens occasionally associated with severe disease, notoriously paralytic poliomyelitis caused by poliovirus. Other enterovirus serotypes such as enterovirus A71 and D68 have been linked to severe neurological syndromes. New enterovirus serotypes continue to emerge, some believed to be derived from nonhuman primates. However, little is known about the circulation patterns of many enterovirus serotypes and, in particular, the detailed enterovirus composition of sewage samples.MethodsWe used a next-generation sequencing approach analyzing reverse transcriptase polymerase chain reaction products synthesized directly from sewage concentrates.ResultsWe determined whole-capsid genome sequences of multiple enterovirus strains from all 4 A to D species present in environmental samples from the United Kingdom, Senegal, and Pakistan.ConclusionsOur results indicate complex enterovirus circulation patterns in human populations with differences in serotype composition between samples and evidence of sustained and widespread circulation of many enterovirus serotypes. Our analyses revealed known and divergent enterovirus strains, some of public health relevance and genetically linked to clinical isolates. Enteroviruses identified in sewage included vaccine-derived poliovirus and enterovirus D-68 stains, new enterovirus A71 and coxsackievirus A16 genogroups indigenous to Pakistan, and many strains from rarely reported serotypes. We show how this approach can be used for the early detection of emerging pathogens and to improve our understanding of enterovirus circulation in humans.
Abstract. An influenza survey was conducted in seven sentinel sites in Dakar, Senegal from June 1996 to December 1998. Throat or nasal swab cultures were randomly collected from 804 patients suffering from influenza-like symptoms. Influenza viruses were isolated at a similar proportion in adults and in children (P ϭ 0.29). Strains of influenza B viruses were isolated from sporadic cases in 1997, whereas type A virus was associated with an isolated peak. Proportions of influenza virus isolation varied from 17.5% to 40.0% between 1996 and 1998 during the peak period (July/September) of acute respiratory infection in Dakar. Rainfall, humidity, and temperatures rose during the same period. Influenza in Dakar seems to be an-all-age groups respiratory infection characterized by high transmission during the hot and rainy season. The antigenic similarity of the A(H3N2) and B viruses to those circulating elsewhere in the world at the same time was confirmed. However, the A(H1N1) strains were found to be more closely related to an Asiatic strain which had not been isolated outside Asia previously. Consequently, the strain close to the A(H1N1)/ Wuhan/371/95 strain isolated in Dakar was included in the composition of the 1998/1999 influenza vaccine. This reinforces the importance of setting up a national influenza control strategy in tropical regions.
Besides polioviruses, non-polio enteroviruses (NPEVs) may also be associated with acute flaccid paralysis (AFP). Because poliomyelitis is on the verge of eradication, more attention should be paid to study NPEVs from non-polio AFP cases and their epidemic patterns. In West African countries the epidemiology of NPEVs remains largely unexplored. We investigated the genetic diversity, frequency, circulation patterns, and molecular epidemiology of NPEVs in seven West African countries by analyzing retrospectively a panel of 3195 stool samples from children with AFP collected through routine poliomyelitis surveillance activities between 2013 and 2014. VP1 sequencing and typing on 201 isolates revealed 39 NPEV types corresponding to EV-A (6.9%), EV-B (90.5%), EV-C (2%) and EV-D (0.5%) species. Echoviruses were isolated most frequently with 138 cases (68.6%), followed by coxsackievirus group B with 35 cases (17.4%). No single NPEV type was remarkably dominant. Interestingly, several rarely described types with limited detection worldwide were identified (EVA76, EVA119, EVB75, EVB77, EVB97, EVC99, CVA20, CVA21 and EVD94). This study demonstrates the extensive diversity and diverse circulation patterns of NPEVs from AFP surveillance and highlights the need to formulate effective long-term strategies to monitor NPEV circulations in West Africa.
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