Oropouche virus cases identified in Ecuador using an optimised qRT-PCR informed by metagenomic sequencing

Abstract

Oropouche virus (OROV) is responsible for outbreaks of Oropouche fever in parts of South America. We recently identified and isolated OROV from a febrile Ecuadorian patient, however, a previously published qRT-PCR assay did not detect OROV in the patient sample. A primer mismatch to the Ecuadorian OROV lineage was identified from metagenomic sequencing data. We report the optimisation of an qRT-PCR assay for the Ecuadorian OROV lineage, which subsequently identified a further five cases in a cohort of 196 febrile patients. We isolated OROV via cell culture and developed an algorithmically-designed primer set for whole-genome amplification of the virus. Metagenomic sequencing of the patient samples provided OROV genome coverage ranging from 68-99%. The additional cases formed a single phylogenetic cluster together with the initial case. OROV should be considered as a differential diagnosis for Ecuadorian patients with febrile illness to avoid mis-diagnosis with other circulating pathogens.

Observational Characterization of the Ecological and Environmental Features Associated with the Presence of Oropouche Virus and the Primary Vector Culicoides paraensis: Data Synthesis and Systematic Review

“…Across all 56 articles included for OROV surveillance, there were eight separate countries where these investigations took place (Figure 3). There were 37 studies performed in Brazil (63%) [2,5,7,16,17,24,32,, followed by 11 studies in Peru (18.6%) [6,18,34,[68][69][70][71][72][73][74][75], with the remaining (18.6%) taking place in Ecuador [3,8,15,70,76], Paraguay [70,77], Suriname [78], Trinidad [4], Bolivia [70], and Costa Rica [79].…”

“…The Orthobunyavirus genus, which consists of 18 serogroups, has been isolated from numerous countries in South America, most commonly Brazil [1][2][3][4][5][6][7][8][9]. The largest serogroup in the Orthobunyavirus genus, the Simbu sergroup, includes viruses associated with both human and animal diseases and is comprised of 25 viruses, including Oropouche virus (OROV) [10,11].…”

“…,15,34,47,49,53-55,60,61,66,72,73,76], or both (13 studies)[4,7,16,17,24,32,42,44,51,56,57,65,70]. Humans were tested for OROV antibodies (11 studies)[5,18,[38][39][40]58,63,64,68,69,78], OROV nucleic acid (19 of studies)[3,6,8,34,43,[47][48][49][53][54][55]59,61,62,66,72,73,76,77], or both (17 studies)[4,7,[15][16][17]24,32,41,…”

Oropouche virus infection in patients with acute febrile syndrome: Is a predictive model based solely on signs and symptoms useful?

“…Furthermore, the incubation period for OROV fever is not precise, however, surveillance conducted during epidemics suggested that it might be between 4 to 8 days [ 4 ]. After this period, infected people present symptoms and develop high viremia, so they can transmit OROV if they are bitten by the vector mosquito [ 19 ]. The acute phase of the disease is between the first 3 to 5 days, an adequate time to collect blood samples from patients with suspected OROV infection and use them in diagnostic methods [ 4 , 12 ].…”

“…The laboratory diagnosis of OROV is carried out through molecular tests such as reverse transcription-polymerase chain reaction (RT-PCR) [ 12 ], real-time PCR (qRT-PCR) [ 19 ], isolation via cell culture [ 20 ], and serological tests with the detection of specific IgM antibodies from blood samples of people with suspected infection by OROV in the acute [ 4 ]. Although they have proven to be successful, they are still limited because they are not available in all countries [ 21 ], due to their high cost andthe lack of trained personnel to carry out the tests [ 14 ].…”