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Review
. 2016 Jun;24(6):490-502.
doi: 10.1016/j.tim.2016.03.003. Epub 2016 Mar 21.

Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses

Shuo Su  1 , Gary Wong  2 , Weifeng Shi  3 , Jun Liu  4 , Alexander C K Lai  5 , Jiyong Zhou  6 , Wenjun Liu  7 , Yuhai Bi  8 , George F Gao  9
Affiliations
Review

Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses

Shuo Su et al. Trends Microbiol. 2016 Jun.

Abstract

Human coronaviruses (HCoVs) were first described in the 1960s for patients with the common cold. Since then, more HCoVs have been discovered, including those that cause severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), two pathogens that, upon infection, can cause fatal respiratory disease in humans. It was recently discovered that dromedary camels in Saudi Arabia harbor three different HCoV species, including a dominant MERS HCoV lineage that was responsible for the outbreaks in the Middle East and South Korea during 2015. In this review we aim to compare and contrast the different HCoVs with regard to epidemiology and pathogenesis, in addition to the virus evolution and recombination events which have, on occasion, resulted in outbreaks amongst humans.

Keywords: MERS; SARS; coronavirus; evolution; pathogenesis; recombination.

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Figures

Figure 1
Figure 1
Global Distribution of Human Coronaviruses. (A) Green, blue, brown, and purple represent the global distribution of the NL63, HKU1, OC43, and 229E human coronaviruses, respectively. (B) Red and yellow represent the global distribution of MERS-CoV and SARS-CoV, respectively.
Figure 2
Figure 2
Intra- and Inter-Species Transmission of Human Coronaviruses. Red, yellow, green, blue, brown, and purple arrows represent transmission of MERS-CoV, SARS-CoV, NL63, HKU1, OC43, and 229E, respectively, between bats, camels, cows, humans, and masked palm civets (shown in a legend on the side of the figure). Unbroken arrows represent confirmed transmission between the two species in question, and broken arrows represent suspected transmission.
Figure 3
Figure 3
Phylogenetic Tree of Known Animal and Human Coronaviruses. Phylogenetic analysis of the full-length genome sequences of coronaviruses publicly available in GenBank was performed using RAxML, with 1000 bootstrap replicates. Lines with different colors represent different coronavirus species, Alpha-coronaviruses (blue lines), Beta-coronaviruses (red lines for Beta-coronavirus C, and black lines for Beta-coronavirus A, B, and D), Gamma-coronaviruses (green lines), and Delta-coronaviruses (purple lines). Human isolates are highlighted with different colors, whereas strains from other hosts are shown in black. Numbers at the branches represent bootstrap values obtained in the phylogenetic analysis.
Figure 4
Figure 4
Key Figure: Genetic Recombination in Human Coronaviruses The colored regions of each human coronavirus indicate genetic recombination at the genomic sites with coronaviruses of zoonotic origin. Specific nucleotide locations where recombination occurred are also shown in broken lines.
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