Phylogeny and COVID-19 The Origins of SARS-CoV-2

ICAP Columbia University, July 22, 2020

Bette KorberLos Alamos National Laboratory

What is a phylogenetic tree?Greek: φῦλον (phûlon), meaning "lineage", and γένεσις (génesis), meaning "origin"

Darwin gets credit for the first one

The relationship between SARS-CoV-1 outbreaksand coronavirus from Palm Civets Song et al., PNAS 102:2430 (2005)

Human, 2002/3

Palm Civet 03Human, 2003/4, GZ

Palm Civet 04, GZ

Common Ancestor

GZ: Guangzhou con

SZ: Shenzhen con

ZS: Zhongshan con

BL1

BL2

BL = Branch length

BL2 reflect the genetic distance from the HP04 leaf to the ancestral nodeBL1+BL2 ~ the genetic distance between PC04 and HP04

What can you learn in glance? HP04’s virus is more closely related to the contemporary Palm Civet, than the virus in people from the year before

Coronavirinae subfamily: 4 genera, RdRpRNA dependent RNA polymerase

Photo credit: Jessicajil

Betacoronavirus

Sarbecovirus

Merbecovirus

From Cui, Li, & Shi, Nature Rev Microbio 17:181 (2019)Origin and evolution of pathogenic coronaviruses

Highly pathogenic in human

Common Cold in human

Common Cold in human

Bats worldwide are a reservoir of highly diverse Alphacoronaviruses and Betacoronaviruses.

2002, 8,098 cases, 9.5% fatal

2012, 2,260 cases, 35.5% fatal

GZ: Guangzhou con

Human, 2002/3Photo credit: Praveenp cc

SZ: Shenzhen conZS: Zhongshan con

Palm Civet

Palm Civet 03Human, 2003/4, GZ

Palm Civet 04, GZ

Horseshoe Bat, reservoir

The relationship between SARS-CoV-1 outbreaksand coronavirus from Palm Civets Song et al., PNAS 102:2430 (2005)

Minor outbreak in Guangzhou markets, Palm Civet -> human

Human, SARS-CoV91 sequences

Recombination is a very important aspect of coronavirus evolution.

Here is a simple example from SAR-CoV-2.

EPI ISL 422850

SARS-CoV-2 sequences from the Netherlands

What do we know about how SARS-CoV-2 evolved and made the jump into humans?

Emergence of SARS-CoV-2 through recombination and strong purifying selection Xiaojun Li, Elena E. Giorgi, Manukumar Honnayakanahalli Marichannegowda, Brian Foley2, ChuanXiao3, Xiang-Peng Kong4, Yue Chen1, S. Gnanakaran2, Bette Korber, Feng Gao

Science Advances, 6:27 eabb9153 (Jul1, 2020)

Maximum likelihood tree, 1000 bootstraps

Sarbecovirus Full Genome tree:

Here we just confirm that Bat RaTG13 isMost closely related to SARS-CoV2 overall.

A pneumonia outbreak associated with a new coronavirusof probable bat origin. Zhou et al. Nature 579, 270–273 (2020)

SARS-CoV2 and SARS-CoV: 79.6% sequence identity

SARS-CoV2 and Bat SL-CoV_RaTG1396.2% sequence identity

Bat SL-CoV_RaTG13:From Rhinolophus affinis from Yunnan province, 2013

2005, Zhejiang China

Guangdong China

Guangxi China

Simplot Analysis Compared to the SARS-CoV-2 Reference strain

Usually closest to RaTG13, but not always.

Full Genome

Bat

Pangolin

RIP analysis comparing Bat RaTG13 and Pangolin GD/P1

Very extensive recombination among Bat and Pangolin sequences in these regions

Very extensive recombination among Bat and Pangolin sequences in these regions

Very extensive recombination among Bat and Pangolin sequences in these regions

The key ACE2 contact residues in SARS-CoV-2match Pangolin P1La

Bat CoVs with large deletions in the ACE2 RBD of the Spike do not infect human cells

Although SARS-CoV-2 and SARS-CoV are very divergent in the ACE2 RBD, they are conformationally highly similar

ACE2

S1 SARS CoVS1 SARS CoV-2

Strong purifying selection with in Group Ain Spike:

SARS COV-2RaTG13Pangolin

Very little nonsynonymous changeExtensive synonymous change

Regi

ons o

f Pur

ifyin

g Se

lect

ion

Simplot showing recombination also played a role in SARS-CoV-1/bat virus evolution

Conclusions

The more efficient cleavage of S1 and S2 subunits of the S glycoprotein and more efficient bindingto ACE2 by SARS-CoV-2 may have allowed SARS-CoV-2 to jump to humans, leading to the rapid

pandemic spread of SARS-CoV-2.

1) Recombination among sarbecoviruses is a very common and critical evolutionary mechanism

2) It is likely that the acquisition of a complete functional RBM by a RaTG13-like CoVthrough a recombination event with a Pan_SL-CoV_GD–like virus enabled SARS-CoV-2 to efficiently use ACE2, thus enabling human infection.

3) SARS-CoV-2 has a unique furin cleavage site insertion (PRRA) not found in Sarbecovirus group, although similar motifs are found in MERS and more divergent bat CoVs, making S1/S2 cleavage in SARSCoV-2 more efficient than in SARS-CoV

Coutard, Antivir Res 176: 104742 (2020)Walls, Cell 180, 281–292.e6

Emergence of SARS-CoV-2 through recombination and strong purifying selection Xiaojun Li, Elena E. Giorgi, Manukumar Honnayakanahalli Marichannegowda, Brian Foley2,

Chuan Xiao3, Xiang-Peng Kong4, Yue Chen1, S. Gnanakaran2, Bette Korber, Feng Gao

Science Advances, 6:27 eabb9153 (Jul1, 2020)