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1.
Biotechnol Genet Eng Rev ; : 1-34, 2022 Aug 28.
Article in English | MEDLINE | ID: covidwho-2004862

ABSTRACT

The question of the origin of coronavirus spread like wildfire ever since it wreaked havoc among humankind, and ever since the scientific community has worked tirelessly to trace the history of the virus. In this review, we have tried to compile relevant literature pertaining to the different theories of origin of SARS-CoV-2, hopefully without any bias, and we strongly support the zoonotic origin of the infamous SARS-CoV-2 in bats and its transfer to human beings through the most probable evolutionary hosts, pangolins and minks. We also support the contemporary 'Circulation Model' that simply mirrors the concept of evolution to explain the origin of the virus which, the authors believe, is the most rational school of thought. The most recent variant of SARS-CoV-2, Omicron, has been taken as an example to clarify the concept. We recommend the community to refer to this model for further understanding and delving deep into this mystery of the origin of SARS-CoV-2.

2.
Genome Biol Evol ; 14(2)2022 02 04.
Article in English | MEDLINE | ID: covidwho-1684680

ABSTRACT

The lack of an identifiable intermediate host species for the proximal animal ancestor of SARS-CoV-2, and the large geographical distance between Wuhan and where the closest evolutionary related coronaviruses circulating in horseshoe bats (members of the Sarbecovirus subgenus) have been identified, is fueling speculation on the natural origins of SARS-CoV-2. We performed a comprehensive phylogenetic study on SARS-CoV-2 and all the related bat and pangolin sarbecoviruses sampled so far. Determining the likely recombination events reveals a highly reticulate evolutionary history within this group of coronaviruses. Distribution of the inferred recombination events is nonrandom with evidence that Spike, the main target for humoral immunity, is beside a recombination hotspot likely driving antigenic shift events in the ancestry of bat sarbecoviruses. Coupled with the geographic ranges of their hosts and the sampling locations, across southern China, and into Southeast Asia, we confirm that horseshoe bats, Rhinolophus, are the likely reservoir species for the SARS-CoV-2 progenitor. By tracing the recombinant sequence patterns, we conclude that there has been relatively recent geographic movement and cocirculation of these viruses' ancestors, extending across their bat host ranges in China and Southeast Asia over the last 100 years. We confirm that a direct proximal ancestor to SARS-CoV-2 has not yet been sampled, since the closest known relatives collected in Yunnan shared a common ancestor with SARS-CoV-2 approximately 40 years ago. Our analysis highlights the need for dramatically more wildlife sampling to: 1) pinpoint the exact origins of SARS-CoV-2's animal progenitor, 2) the intermediate species that facilitated transmission from bats to humans (if there is one), and 3) survey the extent of the diversity in the related sarbecoviruses' phylogeny that present high risk for future spillovers.


Subject(s)
Chiroptera/virology , Coronavirus/genetics , Pangolins/virology , Phylogeny , Recombination, Genetic , Animals , Humans , Phylogeography
3.
Biol Conserv ; 264: 109365, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1487612

ABSTRACT

The Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) prohibits commercial trans-national trade in pangolin specimens. However, African pangolins are continually trafficked to Asia for traditional medicine, with Nigeria considered a key hub. Using reported Nigeria-linked pangolin seizure data and interviews with Nigerian law enforcement officials, we a) characterised Nigeria's involvement in global pangolin trafficking January 2010-September 2021, particularly observing trafficking trends after pangolin's CITES Appendix I listing; b) estimated the minimum number of pangolins whose scales are in Nigeria-linked seizures January 2010-September 2021, and; c) assessed ongoing efforts within Nigeria to curb pangolin trafficking. Nigeria-linked seizures involved 190,407 kg of pangolin derivatives (99.9% scales) from a minimum of 799,343 pangolins (95% confidence interval; 625,944-996,353) of four species (see caveats in Methods). All shipments confiscated in transit were destined for Asia, with a rapid increase in the mass of maritime shipments over time. Furthermore, stockpiling of pangolin derivatives for overseas shipment is perhaps a prominent trafficking model in Nigeria. Nigeria's law enforcement efforts improved from 2017, the same year Nigeria apparently began playing a hub role. The impact of pangolin's CITES Appendix I listing on pangolin trafficking was unclear, as the marked rise in seizures from 2017 when the listing became effective, coincided with improvements in Nigerian law enforcement efforts. COVID-19-induced travel restrictions likely reduced trafficking activities in 2020 but activities may have fully resumed in 2021. This study provides new information to inform effective enforcement and policy formulation efforts to protect African pangolins.

4.
Biodivers Conserv ; 29(13): 3829-3833, 2020.
Article in English | MEDLINE | ID: covidwho-1384497

ABSTRACT

This pandemic situation requests a correct understanding of our impacts on wildlife conservation, which would also provide benefits for our species. In this commentary we revised and discussed some of the repercussions that SARS-CoV-2 pandemic may have to wildlife. We propose four actions that should be taken into account to protect and conserve wildlife in this pandemic era: wildlife "wet" markets must close; human interference with wildlife must be reduced; bats and pangolins must be conserved and not blamed; and Chinese traditional medicine must be more controlled.

5.
Biol Conserv ; 257: 109136, 2021 May.
Article in English | MEDLINE | ID: covidwho-1225150

ABSTRACT

Recent studies have linked COVID-19 induced restrictions to an increase in wildlife crime, with severe yet unknown implications for severely threatened taxa like pangolins. We analyze publicly available online seizure reports involving pangolins across India before (2018-2019) and during the pandemic (March-August 2020), using a longitudinal study design to estimate how lockdowns have impacted pangolin trade. Our analysis indicates a significant increase in seizures reported during the lockdown months of March to August 2020, in comparison to the same period in 2018 and 2019. We discuss the drivers behind this spike in pangolin trade and offer potential conservation measures.

6.
J Med Virol ; 93(1): 499-505, 2021 01.
Article in English | MEDLINE | ID: covidwho-1206790

ABSTRACT

The initial cases of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) occurred in Wuhan, China, in December 2019 and swept the world by 23 June 2020 with 8 993 659 active cases, 469 587 deaths across 216 countries, areas or territories. This strongly implies global transmission occurred before the lockdown of China. However, the initial source's transmission routes of SARS-CoV-2 remain obscure and controversial. Research data suggest bat (RaTG13) and pangolin carried CoV were the proximal source of SARS-CoV-2. In this study, we used systematic phylogenetic analysis of Coronavirinae subfamily along with wild type human SARS-CoV, MERS-CoV, and SARS-CoV-2 strains. The key residues of the receptor-binding domain (RBD) and O-linked glycan were compared. SARS-CoV-2 strains were clustered with RaTG13 (97.41% identity), Pangolin-CoV (92.22% identity) and Bat-SL-CoV (80.36% identity), forms a new clade-2 in lineage B of beta-CoV. The alignments of RBD contact residues to ACE2 justified? Those SARS-CoV-2 strains sequences were 100% identical by each other, significantly varied in RaTG13 and pangolin-CoV. SARS-CoV-2 has a polybasic cleavage site with an inserted sequence of PRRA compared to RaTG13 and only PRR to pangolin. Only serine (Ser) in pangolin and both threonine (Thr) and serine (Ser) O-linked glycans were seen in RaTG13, suggesting that a detailed study needed in pangolin (Manis javanica) and bat (Rhinolophus affinis) related CoV.


Subject(s)
Chiroptera/virology , Coronavirus/genetics , Pangolins/virology , Polysaccharides/chemistry , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Animals , Binding Sites , China , Communicable Disease Control , Coronavirus Envelope Proteins/chemistry , Coronavirus Envelope Proteins/genetics , Gene Expression Regulation, Viral , Host Specificity , Humans , Models, Molecular , Phylogeny , Polysaccharides/metabolism , Protein Conformation , Spike Glycoprotein, Coronavirus/chemistry
7.
J Gen Virol ; 102(4)2021 04.
Article in English | MEDLINE | ID: covidwho-1177362

ABSTRACT

The identification of SARS-CoV-2-like viruses in Malayan pangolins (Manis javanica) has focused attention on these endangered animals and the viruses they carry. We successfully isolated a novel respirovirus from the lungs of a dead Malayan pangolin. Similar to murine respirovirus, the full-length genome of this novel virus was 15 384 nucleotides comprising six genes in the order 3'-(leader)-NP-P-M-F-HN-l-(trailer)-5'. Phylogenetic analysis revealed that this virus belongs to the genus Respirovirus and is most closely related to murine respirovirus. Notably, animal infection experiments indicated that the pangolin virus is highly pathogenic and transmissible in mice, with inoculated mice having variable clinical symptoms and a fatality rate of 70.37 %. The virus was found to replicate in most tissues with the exception of muscle and heart. Contact transmission of the virus was 100 % efficient, although the mice in the contact group displayed milder symptoms, with the virus mainly being detected in the trachea and lungs. The isolation of a novel respirovirus from the Malayan pangolin provides new insight into the evolution and distribution of this important group of viruses and again demonstrates the potential infectious disease threats faced by endangered pangolins.


Subject(s)
Pangolins/virology , Respirovirus Infections , Respirovirus , Animals , Endangered Species , Female , Genome, Viral , Mice , Phylogeny , Respirovirus/classification , Respirovirus/isolation & purification , Respirovirus/pathogenicity , Respirovirus Infections/epidemiology , Respirovirus Infections/veterinary , Respirovirus Infections/virology
8.
Vet Res Commun ; 45(1): 1-19, 2021 Feb.
Article in English | MEDLINE | ID: covidwho-1037288

ABSTRACT

Coronavirus disease-19 (COVID-19) is caused by the severe acute Respiratory syndrome coronavirus-2 (SARS-CoV-2), which has become unstoppable, spreading rapidly worldwide and, consequently, reaching a pandemic level. This review aims to provide the information available so far on the likely animal origin of SARS-CoV-2 and its possible hosts/reservoirs as well as all natural animal infections and experimental evidence using animal models. Horseshoe bats from the species Rhinolophus affinis seem to be a natural reservoir and pangolins (Manis javanica) appear to be an intermediate host of SARS-CoV-2. Humans remain the most likely spreading source of SARS-CoV-2 to other humans and also to domestic, zoo and farm animals. Indeed, human-to-animal transmission has been reported in cats, dogs, tigers, lions, a puma and minks. Animal-to-human transmission is not a sustained pathway, although mink-to-human transmission remains to be elucidated. Through experimental infections, other animals seem also to be susceptible hosts for SARS-CoV-2, namely ferrets, some non-human primate species, hamsters and transgenic mice, while dogs, pigs and poultry are resistant. A One Health perspective must be implemented in order to develop epidemiological surveillance and establish disease control mechanisms to limit zoonotic transmission. Moreover, research in this field is important to better understand SARS-CoV-2 and to obtain the long-awaited vaccine and specific treatment.


Subject(s)
COVID-19/virology , Mammals/virology , SARS-CoV-2/physiology , Animals , COVID-19/transmission , Host Specificity , Humans , Zoonoses
9.
Ecohealth ; 17(3): 406-418, 2020 09.
Article in English | MEDLINE | ID: covidwho-938583

ABSTRACT

The legal and illegal trade in wildlife for food, medicine and other products is a globally significant threat to biodiversity that is also responsible for the emergence of pathogens that threaten human and livestock health and our global economy. Trade in wildlife likely played a role in the origin of COVID-19, and viruses closely related to SARS-CoV-2 have been identified in bats and pangolins, both traded widely. To investigate the possible role of pangolins as a source of potential zoonoses, we collected throat and rectal swabs from 334 Sunda pangolins (Manis javanica) confiscated in Peninsular Malaysia and Sabah between August 2009 and March 2019. Total nucleic acid was extracted for viral molecular screening using conventional PCR protocols used to routinely identify known and novel viruses in extensive prior sampling (> 50,000 mammals). No sample yielded a positive PCR result for any of the targeted viral families-Coronaviridae, Filoviridae, Flaviviridae, Orthomyxoviridae and Paramyxoviridae. In the light of recent reports of coronaviruses including a SARS-CoV-2-related virus in Sunda pangolins in China, the lack of any coronavirus detection in our 'upstream' market chain samples suggests that these detections in 'downstream' animals more plausibly reflect exposure to infected humans, wildlife or other animals within the wildlife trade network. While confirmatory serologic studies are needed, it is likely that Sunda pangolins are incidental hosts of coronaviruses. Our findings further support the importance of ending the trade in wildlife globally.


Subject(s)
Animals, Wild/virology , Pangolins/virology , SARS-CoV-2/isolation & purification , Zoonoses/virology , Animals , Disease Reservoirs/virology , Malaysia , Polymerase Chain Reaction
10.
J Proteome Res ; 19(4): 1351-1360, 2020 04 03.
Article in English | MEDLINE | ID: covidwho-688546

ABSTRACT

As the infection of 2019-nCoV coronavirus is quickly developing into a global pneumonia epidemic, the careful analysis of its transmission and cellular mechanisms is sorely needed. In this Communication, we first analyzed two recent studies that concluded that snakes are the intermediate hosts of 2019-nCoV and that the 2019-nCoV spike protein insertions share a unique similarity to HIV-1. However, the reimplementation of the analyses, built on larger scale data sets using state-of-the-art bioinformatics methods and databases, presents clear evidence that rebuts these conclusions. Next, using metagenomic samples from Manis javanica, we assembled a draft genome of the 2019-nCoV-like coronavirus, which shows 73% coverage and 91% sequence identity to the 2019-nCoV genome. In particular, the alignments of the spike surface glycoprotein receptor binding domain revealed four times more variations in the bat coronavirus RaTG13 than in the Manis coronavirus compared with 2019-nCoV, suggesting the pangolin as a missing link in the transmission of 2019-nCoV from bats to human.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/virology , Genome, Viral/genetics , Host-Pathogen Interactions , Models, Molecular , Pneumonia, Viral/virology , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics , Amino Acid Sequence , Animals , Betacoronavirus/classification , COVID-19 , Eutheria/virology , HIV-1/genetics , Humans , Metagenome , Pandemics , Protein Structure, Tertiary , SARS-CoV-2 , Sequence Alignment , Sequence Analysis, Protein , Snakes/virology
11.
Mol Biol Rep ; 47(6): 4827-4833, 2020 Jun.
Article in English | MEDLINE | ID: covidwho-277073

ABSTRACT

Pangolins, or scaly anteaters, have recently been flagshiped as one of the most illegally traded mammals, and as a corollary, as potential intermediate hosts at the origin of the COVID-19 pandemic. In order to improve the traceability of their trade, we developed 20 polymorphic microsatellite loci for the white-bellied pangolin (Phataginus tricuspis), the species most frequently found on African bushmeat markets. We genotyped 24 white-bellied pangolins from the Douala market, Cameroon, originating from the Ebo forest c. 75 km north-east of Douala. The number of alleles per locus ranged from 4 to 12 (mean = 6.95), and mean observed and expected heterozygosities were 0.592 (0.208-0.875) and 0.671 (0.469-0.836), respectively. Genetic diversity was higher than that cross-estimated from microsatellite loci developed for other species of pangolins. Two loci deviated from Hardy-Weinberg equilibrium and two loci showed linkage disequilibrium. Genetic variance (PCoA) was increased with the addition of 13 pangolins of unknown origin, possibly suggesting that the Douala market is fed from differentiated source populations of white-bellied pangolins. Each of the 37 individuals had a unique multilocus genotype. The unbiased probability of identity (uPI) and the probability of identity among siblings (PIsibs) were both very low (uPI = 8.443 e-21; PIsibs = 1.011 e-07). Only five microsatellite loci were needed to reach the conservative value of PIsibs < 0.01, overall indicating a powerful discriminating power of our combined loci. These 20 newly developed microsatellite loci might prove useful in tracing the local-to-global trade of the white-bellied pangolin, and will hopefully contribute to the DNA-assisted implementation of future conservation strategies at reasonable costs.


Subject(s)
Betacoronavirus/pathogenicity , Coronavirus Infections/transmission , Eutheria/genetics , Microsatellite Repeats , Pandemics , Pneumonia, Viral/transmission , Zoonoses/transmission , Alleles , Animals , COVID-19 , Cameroon/epidemiology , Coronavirus Infections/epidemiology , Coronavirus Infections/prevention & control , Coronavirus Infections/virology , Disease Reservoirs/virology , Eutheria/virology , Female , Genetic Loci , Genetic Markers , Genotype , Humans , Linkage Disequilibrium , Male , Pandemics/prevention & control , Pneumonia, Viral/epidemiology , Pneumonia, Viral/prevention & control , Pneumonia, Viral/virology , SARS-CoV-2 , Zoonoses/epidemiology , Zoonoses/prevention & control , Zoonoses/virology
12.
Trends Microbiol ; 28(7): 515-517, 2020 07.
Article in English | MEDLINE | ID: covidwho-34965

ABSTRACT

The pandemic of coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has posed a severe threat to global public health. Yet, the origin of SARS-CoV-2 remains mysterious. Several recent studies (e.g., Lam et al.,Xiao et al.) identified SARS-CoV-2-related viruses in pangolins, providing novel insights into the evolution and diversity of SARS-CoV-2-related viruses.


Subject(s)
Coronavirus Infections , Coronavirus , SARS Virus , Betacoronavirus , COVID-19 , Humans , Pandemics , Pneumonia, Viral , SARS-CoV-2
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