scholarly journals Coronavirus surveillance in wildlife from two Congo basin countries detects RNA of multiple species circulating in bats and rodents

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0236971
Author(s):  
Charles Kumakamba ◽  
Fabien R. Niama ◽  
Francisca Muyembe ◽  
Jean-Vivien Mombouli ◽  
Placide Mbala Kingebeni ◽  
...  
Keyword(s):  
Pcr Primers ◽  
Congo Basin ◽  
Wild Animals ◽  
Rna Sequences ◽  
Host Diversity ◽  
Frequent Contact ◽  
Human Contact ◽  
Multiple Species ◽  
Ongoing Surveillance ◽  
High Diversity

Coronaviruses play an important role as pathogens of humans and animals, and the emergence of epidemics like SARS, MERS and COVID-19 is closely linked to zoonotic transmission events primarily from wild animals. Bats have been found to be an important source of coronaviruses with some of them having the potential to infect humans, with other animals serving as intermediate or alternate hosts or reservoirs. Host diversity may be an important contributor to viral diversity and thus the potential for zoonotic events. To date, limited research has been done in Africa on this topic, in particular in the Congo Basin despite frequent contact between humans and wildlife in this region. We sampled and, using consensus coronavirus PCR-primers, tested 3,561 wild animals for coronavirus RNA. The focus was on bats (38%), rodents (38%), and primates (23%) that posed an elevated risk for contact with people, and we found coronavirus RNA in 121 animals, of which all but two were bats. Depending on the taxonomic family, bats were significantly more likely to be coronavirus RNA-positive when sampled either in the wet (Pteropodidae and Rhinolophidae) or dry season (Hipposideridae, Miniopteridae, Molossidae, and Vespertilionidae). The detected RNA sequences correspond to 15 alpha- and 6 betacoronaviruses, with some of them being very similar (>95% nucleotide identities) to known coronaviruses and others being more unique and potentially representing novel viruses. In seven of the bats, we detected RNA most closely related to sequences of the human common cold coronaviruses 229E or NL63 (>80% nucleotide identities). The findings highlight the potential for coronavirus spillover, especially in regions with a high diversity of bats and close human contact, and reinforces the need for ongoing surveillance.

scholarly journals Coronavirus surveillance in Congo basin wildlife detects RNA of multiple species circulating in bats and rodents

2020 ◽  
Author(s):  
Charles Kumakamba ◽  
Fabien R. Niama ◽  
Francisca Muyembe ◽  
Jean-Vivien Mombouli ◽  
Placide Mbala Kingebeni ◽  
...  
Keyword(s):  
Pcr Primers ◽  
Congo Basin ◽  
Wild Animals ◽  
Rna Sequences ◽  
Host Diversity ◽  
Frequent Contact ◽  
Human Contact ◽  
Multiple Species ◽  
Ongoing Surveillance ◽  
High Diversity

AbstractCoronaviruses play an important role as pathogens of humans and animals, and the emergence of epidemics like SARS, MERS and COVID-19 is closely linked to zoonotic transmission events primarily from wild animals. Bats have been found to be an important source of coronaviruses with some of them having the potential to infect humans, with other animals serving as intermediate or alternate hosts or reservoirs. Host diversity may be an important contributor to viral diversity and thus the potential for zoonotic events. To date, limited research has been done in Africa on this topic, in particular in the Congo Basin despite frequent contact between humans and wildlife in this region. We sampled and, using consensus coronavirus PCR-primers, tested 3,561 wild animals for coronavirus RNA. The focus was on bats (38%), rodents (38%), and primates (23%) that posed an elevated risk for contact with people, and we found coronavirus RNA in 121 animals, of which all but two were bats. Depending on the taxonomic family, bats were significantly more likely to be coronavirus RNA-positive when sampled either in the wet (Pteropodidae and Rhinolophidae) or dry season (Hipposideridae, Miniopteridae, Molossidae, and Vespertilionidae). The detected RNA sequences correspond to 15 Alpha- and 6 Beta-coronaviruses, with some of them being very similar (>95% nucleotide identities) to known coronaviruses and others being more unique and potentially representing novel viruses. In seven of the bats, we detected RNA most closely related to sequences of the human common cold coronaviruses 229E or NL63 (>80% nucleotide identities). The findings highlight the potential for coronavirus spillover, especially in regions with a high diversity of bats and close human contact, and reinforces the need for ongoing surveillance.

scholarly journals Novel Picobirnaviruses in Respiratory and Alimentary Tracts of Cattle and Monkeys with Large Intra- and Inter-Host Diversity

Viruses ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 574 ◽  
Author(s):  
Patrick C. Y. Woo ◽  
Jade L. L. Teng ◽  
Ru Bai ◽  
Ying Tang ◽  
Annette Y. P. Wong ◽  
...  
Keyword(s):  
Amino Acid ◽  
Positive Sample ◽  
Sequence Type ◽  
Host Diversity ◽  
Respiratory Specimens ◽  
High Diversity

Picobirnaviruses (PBVs) are mostly found in animal alimentary samples. In this study, among 576 respiratory specimens from 476 mammals and 100 chickens, genogroup I PBVs were detected in three cattle and three monkeys, and a genogroup II PBV-positive sample was collected from one cattle specimen. More than one PBV sequence type was observed in two and one genogroup I PBV-positive samples from cattle and monkeys, respectively. Twenty-four complete/near-complete segments 2 (nine from respiratory and 15 from alimentary samples) from the cattle and monkey genogroup I PBVs and one complete segment 2 from the cattle genogroup II PBV were sequenced. Similar to other studies, the cattle PBVs also showed a high diversity. In contrast, the monkey PBVs observed in this study were clustered into three distinct clades. Within each clade, all the sequences showed >99% amino acid identities. This unique phenomenon is probably due to the fact that monkeys in our locality reside in separated troops with minimal inter-troop contact.

scholarly journals High occurrence and unusual serotype diversity of non-typhoidal Salmonella in non-clinical niches, Angola

2016 ◽  
Vol 145 (5) ◽  
pp. 883-886 ◽  
Author(s):  
P. ANTUNES ◽  
J. CAMPOS ◽  
J. MOURÃO ◽  
T. G. RIBEIRO ◽  
C. NOVAIS ◽  
...  
Keyword(s):  
Developing Countries ◽  
African Country ◽  
Animal Health ◽  
Wild Animals ◽  
African Region ◽  
High Occurrence ◽  
Sub Saharan ◽  
First Time ◽  
Comprehensive Surveillance ◽  
High Diversity

SUMMARYNon-typhoidal Salmonella is an important burden, particularly in developing countries of the African region. We report for the first time in Angola, a sub-Saharan African country with commercial/travel relationships with Europe, an unexpectedly high occurrence of Salmonella (n = 12/63, 19%) from a high diversity of sources, particularly farm and wild animals. The detection of diverse serotypes (n = 12), involving putative new S. enterica subsp. salamae serotypes, is also of note, reinforcing the need for a comprehensive surveillance in Angola critical to identify animal/food/environmental sources of salmonellosis with impact on animal health, local people, tourists and exported products.

scholarly journals Evaluation of haplotype callers for next-generation sequencing of viruses

2019 ◽  
Author(s):  
Anton Eliseev ◽  
Keylie M. Gibson ◽  
Pavel Avdeyev ◽  
Dmitry Novik ◽  
Matthew L. Bendall ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Haplotype Reconstruction ◽  
Reconstruction Accuracy ◽  
Effective Population ◽  
Host Diversity ◽  
Reconstruction Methods ◽  
True Number ◽  
Generation Sequencing ◽  
Hiv 1 ◽  
High Diversity

AbstractCurrently, the standard practice for assembling next-generation sequencing (NGS) reads of viral genomes is to summarize thousands of individual short reads into a single consensus sequence, thus confounding useful intra-host diversity information for molecular phylodynamic inference. It is hypothesized that a few viral strains may dominate the intra-host genetic diversity with a variety of lower frequency strains comprising the rest of the population. Several software tools currently exist to convert NGS sequence variants into haplotypes. However, previous studies suggest that current approaches of haplotype reconstruction greatly underestimate intra-host diversity. Here, we tested twelve NGS haplotype reconstruction methods using viral populations simulated under realistic evolutionary dynamics. Parameters for the simulated data spanned known fast evolving viruses (e.g., HIV-1) diversity estimates to test the limits of the haplotype reconstruction methods and ensured coverage of predicted intra-host viral diversity levels. Using those parameters, we simulated HIV-1 viral populations of 216-1,185 haplotypes per host at a frequency <7%. All twelve investigated haplotype callers showed variable performance and produced drastically different results that were mainly driven by differences in mutation rate and, to a lesser extent, in effective population size. Most methods were able to accurately reconstruct haplotypes when genetic diversity was low. However, under higher levels of diversity (e.g., those seen intra-host HIV-1 infections), haplotype reconstruction accuracy was highly variable and, on average, poor. High diversity levels led to severe underestimation of, with a few tools greatly overestimating, the true number of haplotypes. PredictHaplo and PEHaplo produced estimates close to the true number of haplotypes, although their haplotype reconstruction accuracy was worse than that of the other ten tools. We conclude that haplotype reconstruction from NGS short reads is unreliable due to high genetic diversity of fast-evolving viruses. Local haplotype reconstruction of longer reads to phase variants may provide a more reliable estimation of viral variants within a population.HighlightsHaplotype callers for NGS data vary greatly in their performance.Haplotype callers performance is mainly determined by mutation rate.Haplotype callers performance is less sensitive to effective population size.Most haplotype callers perform well with low diversity and poorly with high diversity.PredictHaplo performs best if genetic diversity is in the range of HIV diversity.

scholarly journals Primaclade--a flexible tool to find conserved PCR primers across multiple species

2004 ◽  
Vol 21 (7) ◽  
pp. 1263-1264 ◽  
Author(s):  
M. D. Gadberry ◽  
S. T. Malcomber ◽  
A. N. Doust ◽  
E. A. Kellogg
Keyword(s):  
Pcr Primers ◽  
Flexible Tool ◽  
Multiple Species

Great Apes as Food

2003 ◽  
Vol 3 (2) ◽  
pp. 64-70 ◽  
Author(s):  
Dale Peterson
Keyword(s):  
Human Population ◽  
Food Source ◽  
Great Apes ◽  
Modern Human ◽  
Ethical Concern ◽  
Congo Basin ◽  
Cultural Tradition ◽  
Wild Animals ◽  
Great Ape ◽  
Sustainable Food

People living in or on the edges of the world's great forests have always taken the protein offered by wild animals; thus the three African great ape species - chimpanzees, bonobos, and gorillas - are by long-standing cultural tradition eaten by many ethnic groups living in Central Africa's Congo Basin. Today, with modern human population growth, modern hunting technologies, and especially with the unprecedented opening of these forests via roads cut by European and Asian loggers, an exploding game meat (or "bushmeat") commerce into the big cities threatens the very existence of those three charismatic species. What until recently was a sustainable food practice has recently become catastrophically unsustainable. The author identifies some of the traditional logic in favor of using apes as a food source and describes three contemporary arguments against it: the practice threatens African biodiversity; challenges public health (among other things, the continuing potential for Ebola transmission or the creation of an aggressive new HIV strain); and it remains (since genetic analysis now clarifies that the apes are so very close to human) a matter of legitimate ethical concern.

scholarly journals Genomic history of human monkey pox infections in the Central African Republic between 2001 and 2018

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nicolas Berthet ◽  
Stéphane Descorps-Declère ◽  
Camille Besombes ◽  
Manon Curaudeau ◽  
Andriniaina Andy Nkili Meyong ◽  
...  
Keyword(s):  
Central African Republic ◽  
Democratic Republic Of Congo ◽  
Central Africa ◽  
Armed Conflicts ◽  
Molecular Dating ◽  
Congo Basin ◽  
Wild Animals ◽  
Population Movements ◽  
History Of ◽  
Northern Edge

AbstractMonkeypox is an emerging infectious disease, which has a clinical presentation similar to smallpox. In the two past decades, Central Africa has seen an increase in the frequency of cases, with many monkeypox virus (MPXV) isolates detected in the Democratic Republic of Congo (DRC) and the Central African Republic (CAR). To date, no complete MPXV viral genome has been published from the human cases identified in the CAR. The objective of this study was to sequence the full genome of 10 MPXV isolates collected during the CAR epidemics between 2001 and 2018 in order to determine their phylogenetic relationships among MPXV lineages previously described in Central Africa and West Africa. Our phylogenetic results indicate that the 10 CAR isolates belong to three lineages closely related to those found in DRC. The phylogenetic pattern shows that all of them emerged in the rainforest block of the Congo Basin. Since most human index cases in CAR occurred at the northern edge of western and eastern rainforests, transmissions from wild animals living in the rainforest is the most probable hypothesis. In addition, molecular dating estimates suggest that periods of intense political instability resulting in population movements within the country often associated also with increased poverty may have led to more frequent contact with host wild animals. The CAR socio-economic situation, armed conflicts and ecological disturbances will likely incite populations to interact more and more with wild animals and thus increase the risk of zoonotic spillover.

scholarly journals Aedes aegypti from Amazon Basin Harbor High Diversity of Novel Viral Species

Viruses ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 866
Author(s):  
Geovani de Oliveira Ribeiro ◽  
Vanessa S. Morais ◽  
Fred Julio Costa Monteiro ◽  
Edcelha Soares D’Athaide Ribeiro ◽  
Marlisson Octavio da S Rego ◽  
...  
Keyword(s):  
Aedes Aegypti ◽  
Amazon Basin ◽  
Virus Species ◽  
Rna Sequences ◽  
Invertebrate Diversity ◽  
Wide Range ◽  
Novel Virus ◽  
Medical Importance ◽  
Amazonian Region ◽  
High Diversity

Viruses are the most diverse and abundant microorganisms on earth, highly adaptive to a wide range of hosts. Viral diversity within invertebrate hosts has gained notoriety in recent years in public health as several such viruses have been of medical importance. Aedes aegypti serves as a vector for several viruses that have caused epidemics within the last year throughout Brazil; including Dengue, Zika and Chikungunya. This study aimed to identify new viral agents within Aedes aegypti mosquito in a city of the Amazonian region, where it is highly endemic. Metagenomic investigation was performed on 60 mosquito pools and viral RNA sequences present in their microbiota were characterized using genomic and phylogenetic tools. In total, we identified five putative novel virus species related to the Sobemovirus genus, Iflavirus genus and Permutatetraviridae family. These findings indicate a diverse taxonomy of viruses present in the mosquito microbiota of the Amazon, the region with the greatest invertebrate diversity in the world.

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