An epidemiological investigation of a multisource outbreak of Crimean-Congo hemorrhagic fever in Karachi, from January– 15th September 2016

Abstract

Purpose: Examining the viral diversity present in domestic and wild birds in Brazil. To this end we applied a metagenomic approach to clinical specimens derived from different birds species in various geographical locations.Methods & Materials: We sampled 100 individuals that represented eight different birds species. The samples of poultry (Gallus gallus, Cairina monchata) were collected in Breves city, Pará State, whereas samples from migratory birds (Arenaria interpres, Thalasseus sandvicensis, Calidris pusilla) were collected in Coroa do Avião Island, Pernambuco State, and wild residents birds (Hilophilus amaurocephalus, Sarkesphorus cristapus and Coryphospingus pileatus) in São José do Egito, Paraíba State. Samples were distributed in pools based on species, sample type (i.e. cloacal swabs and sera), date and capture location. Viral RNA was extracted and followed by synthesis of double-stranded cDNA prior to Illumina sequencing. Sequence reads were quality-filtered, removed the adapter sequences and remaining reads were assembled de novo. Obtained contigs were submitted to BLAST-based searches to identify viruses and further subject to phylogenetic analyses.Results: We found nine viruses that showed similarity to known caliciviruses and astroviruses. A complete genome and two partial genomes of astrovirus were obtained from two pools of Arenaria interpres. The genome organization of Arenaria interpres astrovirus (AiAstV) was similar to that of other Astrovirus, and phylogenetic analysis reveals that the AiAstV is a member of Avastrovirus genus. AiAstV was most closely related to a recently characterized chicken avastrovirus with their genomes sharing ∼60% amino acid identity. On another hand, four contigs and a complete genome of a calivirus were obtained in four pools from Cairina monchata, Arenaria interpres and Hilophilus amaurocephalus. A complete full-length genome sequence of approximately 8 kb in length was obtained from samples from Arenaria interpres, showing a genomic organization typical of caliciviruses. Phylogenetic analysis reveals that Arenaria interpres calicivirus is a potential member of Nacovirus genus. Interestingly, both novel viruses were detected exclusively from cloacals swab, strongly suggesting the excretion of these viruses in nature. Conclusion:Based on our results we found two novel astrovirus and calicivirus species in the Avastrovirus and Nacovirus genera, respectively. Further studies should aim to characterize their host range and pathogenic potential.

NTDs in the age of urbanization, climate change, and conflict: Karachi, Pakistan as a case study

“…There also proved to be a significant number of WNVdengue coinfections, many of which were associated with neurological symptoms in affected patients [60]. Other studies have also helped confirm the presence of WNV and JEV in the mosquito vector population of the city [29,32] A multisource outbreak of Crimean-Congo hemorrhagic fever (CCHF) was reported in Karachi in 2016, with a high case fatality rate of 75% [61]. Of the 8 confirmed CCHF cases at various health facilities in Karachi, the majority of patients were males engaged in animal trading activities in the city [61].…”

“…A multisource outbreak of Crimean–Congo hemorrhagic fever (CCHF) was reported in Karachi in 2016, with a high case fatality rate of 75% [ 61 ]. Of the 8 confirmed CCHF cases at various health facilities in Karachi, the majority of patients were males engaged in animal trading activities in the city [ 61 ].…”