Seroevidence of Zoonotic Viruses in Rodents and Humans in Kibera Informal Settlement, Nairobi, Kenya

Rodents are known reservoir hosts for a number of pathogens that can spillover into humans and cause disease. These threats are likely to be elevated in informal urban settlements (i.e., slums), where rodent and human densities are often high, rodents live in close proximity to humans, and human knowledge of disease risks and access to health care is often limited. While recent research attention has focused on zoonotic risks posed by urban rodents in major cities around the world, informal urban settlements have received far less attention. Here we report on a study in which samples were collected from 195 commensal rodents and 124 febrile human patients in the Kibera informal settlement in Nairobi, Kenya (one of the largest informal urban settlements in the world). Using immunofluorescence assays, samples were screened for antibodies against common rodent-borne zoonotic virus groups, namely orthopoxviruses, arenaviruses, and hantaviruses. We detected antibodies against orthopoxviruses in rodents (4.1% positive) and antibodies in humans against orthopoxviruses, arenaviruses, and hantaviruses (4.8%, 3.2%, and 8.1% positive, respectively). No rodents had antibodies against arenaviruses or hantaviruses. These results provide strong evidence for the circulation of zoonotic viruses in rodents and humans in Kibera urban settlement, but discordance between viruses detected in host groups indicates that other species or taxa may also serve as reservoirs for these zoonotic viruses or that humans testing positive could have been exposed outside of the Kibera settlement. More broadly, this study highlights the threat posed by zoonotic viruses in informal urban settlements and the need to mitigate human exposure risks.Peer reviewe

Seroevidence of Zoonotic Viruses in Rodents and Humans in Kibera Informal Settlement, Nairobi, Kenya

Rodents are known reservoir hosts for a number of pathogens that can spillover into humans and cause disease. These threats are likely to be elevated in informal urban settlements (i.e., slums), where rodent and human densities are often high, rodents live in close proximity to humans, and human knowledge of disease risks and access to health care is often limited. While recent research attention has focused on zoonotic risks posed by urban rodents in major cities around the world, informal urban settlements have received far less attention. Here we report on a study in which samples were collected from 195 commensal rodents and 124 febrile human patients in the Kibera informal settlement in Nairobi, Kenya (one of the largest informal urban settlements in the world). Using immunofluorescence assays, samples were screened for antibodies against common rodent-borne zoonotic virus groups, namely orthopoxviruses, arenaviruses, and hantaviruses. We detected antibodies against orthopoxviruses in rodents (4.1% positive) and antibodies in humans against orthopoxviruses, arenaviruses, and hantaviruses (4.8%, 3.2%, and 8.1% positive, respectively). No rodents had antibodies against arenaviruses or hantaviruses. These results provide strong evidence for the circulation of zoonotic viruses in rodents and humans in Kibera urban settlement, but discordance between viruses detected in host groups indicates that other species or taxa may also serve as reservoirs for these zoonotic viruses or that humans testing positive could have been exposed outside of the Kibera settlement. More broadly, this study highlights the threat posed by zoonotic viruses in informal urban settlements and the need to mitigate human exposure risks.Peer reviewe

Serological Evidence of Exposure to Onyong-Nyong and Chikungunya Viruses in Febrile Patients of Rural Taita-Taveta County and Urban Kibera Informal Settlement in Nairobi, Kenya

Several alphaviruses, such as chikungunya (CHIKV) and Onyong-nyong (ONNV), are endemic in Kenya and often cause outbreaks in different parts of the country. We assessed the seroprevalence of alphaviruses in patients with acute febrile illness in two geographically distant areas in Kenya with no previous record of alphavirus outbreaks. Blood samples were collected from febrile patients in health facilities located in the rural Taita-Taveta County in 2016 and urban Kibera informal settlement in Nairobi in 2017 and tested for CHIKV IgG and IgM antibodies using an in-house immunofluorescence assay (IFA) and a commercial ELISA test, respectively. A subset of CHIKV IgG or IgM antibody-positive samples were further analyzed using plaque reduction neutralization tests (PRNT) for CHIKV, ONNV, and Sindbis virus. Out of 537 patients, 4 (0.7%) and 28 (5.2%) had alphavirus IgM and IgG antibodies, respectively, confirmed on PRNT. We show evidence of previous and current exposure to alphaviruses based on serological testing in areas with no recorded history of outbreaks.Peer reviewe

Serological Evidence of Exposure to Onyong-Nyong and Chikungunya Viruses in Febrile Patients of Rural Taita-Taveta County and Urban Kibera Informal Settlement in Nairobi, Kenya

Several alphaviruses, such as chikungunya (CHIKV) and Onyong-nyong (ONNV), are endemic in Kenya and often cause outbreaks in different parts of the country. We assessed the seroprevalence of alphaviruses in patients with acute febrile illness in two geographically distant areas in Kenya with no previous record of alphavirus outbreaks. Blood samples were collected from febrile patients in health facilities located in the rural Taita-Taveta County in 2016 and urban Kibera informal settlement in Nairobi in 2017 and tested for CHIKV IgG and IgM antibodies using an in-house immunofluorescence assay (IFA) and a commercial ELISA test, respectively. A subset of CHIKV IgG or IgM antibody-positive samples were further analyzed using plaque reduction neutralization tests (PRNT) for CHIKV, ONNV, and Sindbis virus. Out of 537 patients, 4 (0.7%) and 28 (5.2%) had alphavirus IgM and IgG antibodies, respectively, confirmed on PRNT. We show evidence of previous and current exposure to alphaviruses based on serological testing in areas with no recorded history of outbreaks.Peer reviewe

High prevalence of an alpha variant lineage with a premature stop codon in ORF7a in Iraq, winter 2020–2021

Publisher Copyright: Copyright: © 2022 Al-Rashedi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Since the first reported case of coronavirus disease 2019 (COVID-19) in China, SARS-CoV-2 has been spreading worldwide. Genomic surveillance of SARS-CoV-2 has had a critical role in tracking the emergence, introduction, and spread of new variants, which may affect transmissibility, pathogenicity, and escape from infection or vaccine-induced immunity. As anticipated, the rapid increase in COVID-19 infections in Iraq in February 2021 is due to the introduction of variants of concern during the second wave of the COVID-19 pandemic. To understand the molecular epidemiology of SARS-CoV-2 during the second wave in Iraq (2021), we sequenced 76 complete SARS-CoV-2 genomes using NGS technology and identified genomic mutations and proportions of circulating variants among these. Also, we performed an in silico study to predict the effect of the truncation of NS7a protein (ORF7a) on its function. We detected nine different lineages of SARS-CoV-2. The B.1.1.7 lineage was predominant (80.20%) from February to May 2021, while only one B.1.351 strain was detected. Interestingly, the phylogenetic analysis showed that multiple strains of the B.1.1.7 lineage clustered closely with those from European countries. A notable frequency (43.33%) of stop codon mutation (NS7a Q62stop) was detected among the B.1.1.7 lineage sequences. In silico analysis of NS7a with Q62stop found that this stop codon had no considerable effect on the function of NS7a. This work provides molecular epidemiological insights into the spread variants of SARS-CoV-2 in Iraq, which are most likely imported from Europe.Peer reviewe

Bombali Virus in Mops condylurus Bat, Kenya

Bombali virus (genus Ebolavirus) was identified in organs and excreta of an Angolan free-tailed bat (Mops condylurus) in Kenya. Complete genome analysis revealed 98% nucleotide sequence similarity to the prototype virus from Sierra Leone. No Ebola virus-specific RNA or antibodies were detected from febrile humans in the area who reported contact with bats.Peer reviewe

Serologic Surveillance for SARS-CoV-2 Infection among Wild Rodents, Europe

Publisher Copyright: © 2022 Centers for Disease Control and Prevention (CDC). All rights reserved.Peer reviewe

The phylodynamics of SARS-CoV-2 during 2020 in Finland

Finland has had a low incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infections as compared to most European countries. Here we report the origins and turnover of SARS-CoV-2 lineages circulating in Finland in 2020. SARS-CoV-2 introduced to Finland in January 2020 and spread rapidly across southern Finland during spring. We observed rapid turnover among Finnish lineages during this period. Clade 20C became the most prevalent among sequenced cases and was replaced by other strains in fall 2020. Bayesian phylogeographic reconstructions suggested 42 independent introductions into Finland during spring 2020, mainly from Italy, Austria, and Spain, which might have been the source for a third of cases. The investigations of the original introductions of SARS-CoV-2 to Finland during the early stages of the pandemic and of the subsequent lineage dynamics could be utilized to assess the role of transboundary movements and effects of early intervention and public health measures.Peer reviewe

Characterization of novel LCMV strains in Southern Iraq

LCMV Lymphocytic choriomeningitis virus is a rodent-borne pathogen belongs to Arenaviridae family. Most of the studies have referred Mus musculus as the main reservoir of the LCMV. It has been detected in pet rodents, laboratory rodents, and wild mice. Humans be infected with LCMV through the ingestion or inhalation of sources contaminated with rodent feces, urine, or both. LCMV infection can be asymptomatic, present with mild symptoms, or it can cause aseptic meningoencephalitis (AME) and teratogenic effects in infants. However, clinical cases of LCMV infection have been rarely reported, and there is only fragmental knowledge on the presence and prevalence of LCMV infections around the world. Likewise, the genetic characteristics of the circulating LCMV strains and impact of LCMV on public health have remained poorly characterized. This study was performed in the Southern Iraq, due to the lack of comprehensive information about LCMV in this area. There were three main aims in this thesis. First, to assess the prevalence of LCMV among the healthy human population in the Nasiriyah region, southern Iraq. Second, to assess whether LCMV infections can be associated with neurological manifestations. Third, to characterize the genetic variation and evolutionary history of LCMV strains circulating in southern Iraq. Serum and CSF samples were collected from patients and healthy people in Nasiriyah governorate in the Southern Iraq. Serum samples were screened for LCMV using Immunofluorescence assay (IFA) to detect IgG and IgM antibodies. Real-time PCR was used to detect LCMV genome. In order to confirm the PCR positive samples, we sequenced these samples by Next-generation sequencing. The serological assay results showed 12.22% IgG prevalence of LCMV among healthy people and 7.36% IgG prevalence among patients with neurological symptoms. The IgM prevalence was 1.25% among the patients with acute infections. From symptomatic patients, we sequenced partial L-segments of two new LCMV strains. The phylogenetic tree constructed on the basis of all known LCMV strains suggested that these new LCMV strains from Iraq are genetically distant from the previously known LCMV strains and form a novel sub-cluster within LCMV species. This study is the first survey of LCMV in the Southern Iraq. LCMV appears to be a rather common infection in Iraq. I reported new strains of LCMV that are circulating in the study site and most likely is the causative agent of the central nervous system-associated clinical manifestations in these patients. For future work, I’m aiming the detection of other Arenaviruses spreading in the Southern Iraq

Lymphocytic Choriomeningitis Virus Infections and Seroprevalence, Southern Iraq

Acute febrile neurological infection cases in southern Iraq (N = 212) were screened for lymphocytic choriomeningitis virus (LCMV). Two LCMV IgM–positive serum samples and 2 cerebrospinal fluid samples with phylogenetically distinct LCMV strains were found. The overall LCMV seroprevalence was 8.8%. LCMV infections are common and associated with acute neurological disease in Iraq.Peer reviewe