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Ultrastructural Evidence for Direct Renal Infection with

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SARS-CoV-2
Evan A. Farkash,1 Allecia M. Wilson,1,2 and Jeffrey M. Jentzen1,2
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1
Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
2
Washtenaw County Medical Examiner’s Office, Ann Arbor, Michigan

ABSTRACT
Background A significant fraction of patients with coronavirus disease 2019 to 8.75) for stage 2 and 3 AKI, respec-
(COVID-19) display abnormalities in renal function. Retrospective studies of patients tively. 1 Preexisting renal disease may
hospitalized with COVID-19 in Wuhan, China, report an incidence of 3%–7% pro- also present an increased risk for poor
gressing to ARF, a marker of poor prognosis. The cause of the renal failure in COVID- outcome, with an adjusted hazard ratio
19 is unknown, but one hypothesized mechanism is direct renal infection by the of 2.0 (95% CI, 1.32 to 3.15) for hospi-
causative virus, SARS-CoV-2. talized patients. Various mechanisms for
Methods We performed an autopsy on a single patient who died of COVID-19 after kidney injury in COVID-19 have been
open repair of an aortic dissection, complicated by hypoxic respiratory failure and proposed, including ischemic injury ow-
oliguric renal failure. We used light and electron microscopy to examine renal tissue ing to multiorgan failure, inflammatory
for evidence of SARS-CoV-2 within renal cells. injury secondary to cytokine storm, and
direct infection.2,8 Immunohistochemi-
Results Light microscopy of proximal tubules showed geographic isometric vacuo-
cal and PCR-based approaches are possi-
lization, corresponding to a focus of tubules with abundant intracellular viral arrays.
ble approaches to demonstrate direct
Individual viruses averaged 76 mm in diameter and had an envelope studded with
renal infection by severe acute respira-
crown-like, electron-dense spikes. Vacuoles contained double-membrane vesicles
tory syndrome coronavirus 2 (SARS-
suggestive of partially assembled virus.
CoV-2), but both could be confounded
Conclusions The presence of viral particles in the renal tubular epithelium that were by either filtration of circulating viral an-
morphologically identical to SARS-CoV-2, and with viral arrays and other features of tigens or incidental detection of nucleic
virus assembly, provide evidence of a productive direct infection of the kidney by acids in plasma. Detection of virus within
SARS-CoV-2. This finding offers confirmatory evidence that direct renal infection renal cells by electron microscopy has
occurs in the setting of AKI in COVID-19. However, the frequency and clinical sig- been proposed as a straightforward ap-
nificance of direct infection in COVID-19 is unclear. Tubular isometric vacuolization proach to demonstrate direct renal
observed with light microscopy, which correlates with double-membrane vesicles involvement.
containing vacuoles observed with electronic microscopy, may be a useful histologic
marker for active SARS-CoV-2 infection in kidney biopsy or autopsy specimens.
JASN 31: 1683–1687, 2020. doi: https://doi.org/10.1681/ASN.2020040432 CLINICAL PRESENTATION

A 53-year-old male with a history of obe-

The association between coronavirus
disease 2019 (COVID-19) and ARF is
an evolving area of study. Renal dysfunc-
tion is common in COVID-19, with a
sizeable fraction of patients presenting
with proteinuria or elevated BUN. 1,2
A minority of patients progress to more
severe renal disease; retrospective studies
of patients hospitalized with COVID-19
in Wuhan, China, report an incidence of
ARF ranging from 3% to 7%.3–6 Early
data from Italy suggests a correlation be-
tween kidney injury and overall disease
severity, with renal failure up to four
times more common in patients in in-
tensive care units relative to hospitalized
patients not requiring intensive care unit
admission.7 Renal failure in COVID-19
appears to be an independent risk factor
for death in hospitalized patients, with re-
ported adjusted hazard ratios of 3.5 (95%
CI, 1.50 to 8.27) and 4.7 (95% CI, 2.55
sity, hyperlipidemia, and a recent sick
Received April 10, 2020. Accepted April 20, 2020.
Published online ahead of print. Publication date
available at www.jasn.org.
Correspondence: Dr. Evan Farkash, Department of
Pathology, University of Michigan Medical School,
7520 MSRB1, 1150 W. Medical Center Dr, Ann
Arbor, MI 48109. Email: efarkash@med.umich.edu
Copyright © 2020 by the American Society of
Nephrology

JASN 31: 1683–1687, 2020 ISSN : 1046-6673/3108-1683 1683

 RAPID COMMUNICATION www.jasn.org
contact presented with an acute type A
aortic dissection, extending from the si-
notubular junction to the iliac bifurca-
tion, with compression of the right renal
artery. On angiogram, renal arteries had
a beaded appearance suspicious for fi-
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bromuscular dysplasia. The dissection
was repaired via median sternotomy
with ascending and hemiarch aortic re-
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placement, and the patient was dis-
charged to intensive care on mechanical
ventilation. His postoperative course
was notable for leukocytosis (white
blood cell count of 14,000–18,000 per
ml) and persistently elevated fraction of
inspired oxygen requirements. On the
fourth postoperative day he was success-
fully extubated but remained oxygen-
dependent on high-flow nasal cannula
and Bilevel Positive Airway Pressure.
On the sixth postoperative day, the
patient’s hypoxemia progressed, requir-
ing reintubation as well as inhaled
nitrous oxide. A chest x-ray showed bi-
lateral patchy opacities, a PCR respira-
tory viral panel was negative, and a
locally performed RT-PCR was positive
for SARS-CoV-2. He was initially treated
with hydroxychloroquine 600 mg twice
daily, then 200 mg three times daily for 3
days. In addition, he enrolled in a ran-
domized, controlled trial of sarilumab
(IL-6 inhibitor), although it is not
known whether he received therapy or
placebo. Despite therapy, the patient de-
veloped multiorgan dysfunction, with
mildly elevated liver enzymes and new-
onset diabetes. On the 11th postopera-
tive day, his respiratory and renal status
worsened with progressive hypoxemia
and acidosis recalcitrant to intravenous
bicarbonate.
The patient’s renal function closely
mirrored his respiratory function (Fig-
ure 1). Initially, his eGFR declined
acutely after the cardioplegic aortic re-
pair, from 42 ml/min per 1.73 m2 on
admission to 29 ml/min per 1.73 m2.
In the setting of diuresis with furosemide
and metolazone on postoperative day 4,
his eGFR further declined to 17 ml/min
per 1.73 m2. His renal function briefly
improved (eGFR 22 ml/min per
1.73 m2), but subsequently deteriorated
on postoperative day 6, simultaneous
1684 JASN
with the development of acute respira-
tory distress. Over the course of his ill-
ness, his urine output remained between
2 and 4 L per day, but on the 11th post-
operative day he became acutely oliguric
(100 ml/d), and continuous RRTwas ini-
tiated in the setting of acidosis and de-
clining respiratory status.
The patient died of cardiac arrest on
the 12th postoperative day, and an au-
topsy was performed in a negative pres-
sure suite, with renal tissue taken for
light and electron microscopy. Because
of the risk of infectious aerosols, the au-
topsy was limited to the chest and abdo-
men, and routine protective equipment
(N95 respirator, gown, double gloves,
and eye protection) was supplemented
with face shields and disposable full-
body suits.
RESULTS
At autopsy, the lungs showed gross and
microscopic evidence of diffuse acute al-
veolar damage with well formed hyaline
membranes, edema, and early acute
bronchopneumonia, consistent with
early reports of patient deaths after
SARS-CoV-2 infection. The left and
right kidneys weighed 230 g and 240 g,
respectively, and were grossly unremark-
able. Light microscopic examination of
formalin-fixed paraffin sections of the
kidneys showed mild autolysis, with no
definitive nuclear inclusions (not
shown). There was no evidence of glo-
merulitis, FSGS, or a tubulointerstitial
inflammatory infiltrate. Of note, some
of the toluidine blue–stained epoxy sec-
tions showed focal tubular isometric va-
cuolization (Figure 2A). Other epoxy
sections showed mild-to-moderate ne-
crosis and karyolysis more typical for is-
chemic injury/autolysis (Figure 2B).
Ultrastructural analysis, limited to
the kidney, revealed abundant viral
forms within tubular epithelial cells in
one of three examined blocks, correlat-
ing directly to the areas of isometric
vacuolization (Figure 3A). Individual vi-
ruses ranged in size from 65 to 91 nm
(mean 76 nm). Mature-appearing viru-
ses were predominantly located within
Significance Statement
The cause of kidney injury in COVID-19 is
unclear. In an autopsy study of a single
patient with COVID-19 and acute oliguric
renal failure, the authors identified intra-
cellular viral arrays within proximal tubu-
lar epithelial cells by electron microscopy,
consistent with direct infection of the kidney
by SARS-CoV-2. They also found ultrastruc-
tural features similar to those described in
reports of kidney cell lines infected with the
related SARS-CoV-1 virus. Virally infected
tubular cells showed isometric vacuolization
on light microscopy. These findings provide
confirmatory evidence of direct kidney in-
fection by SARS-CoV-2 in a patient. How-
ever, this work does not exclude other
causes of kidney injury, and additional study
is needed to determine the frequency and
clinical significance of direct kidney in-
fection on renal failure in COVID-19.
the cytoplasm, focally organized into
small arrays (Figure 3B). Viral particles
were composed of cores with intermediate
electron density, surrounded by an enve-
lope studded with abundant crown-like,
electron-dense spikes (Figure 3C). Adja-
cent vacuoles contained abundant ovoid
double-membrane vesicles associated
with rough endoplasmic reticulum, rep-
resenting possible viral assembly
(Figure 3D). Examined glomeruli and
vascular endothelial cells were negative
for virus, and coronavirus was not
identified in tubular epithelium with
more conventional injury and necrosis
by light microscopy.
DISCUSSION
There are currently multiple plausible
mechanisms for renal injury in
COVID-19, including ischemic injury,
cytokine storm, and direct infection.
Previous research has established a po-
tential mechanism for kidney infection
by SARS-CoV-2. The receptor for SARS-
CoV-2 cellular entry is angiotensin-
converting enzyme 2, which is present
at high concentrations in the brush bor-
ders of renal tubular epithelial cells, and
at lower levels in glomerular and vascu-
lar endothelial cells. 9 In vitro experi-
ments have demonstrated SARS-CoV-2
JASN 31: 1683–1687, 2020
 www.jasn.org RAPID COMMUNICATION

45

COVID-19 positive,
40

Reintubated
35

Extubated
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eGFR (mL/min/1.73m2)

30

CRRT initiated
25
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20

15

10

0
0 1 2 3 4 5 6 7 8 9 10 11 12 13
Postoperative day

Figure 1. Kidney function recrudescence with diagnosis of COVID-19. The patient’s eGFR over the course of hospitalization, measured
from admission for aortic repair on day 0. eGFR calculated by the Chronic Kidney Disease Epidemiology Collaboration equation. CRRT,
continuous RRT.

viral infection and replication within
Vero cells, a primate kidney epithelial
cell line.10,11 In humans, SARS-CoV-2
was initially detected by RT-PCR in the
urine of a minority of patients with
COVID-19; although other studies
show no detectible urine shedding.12,13
Recently, Su et al.14 demonstrated coro-
navirus by electron microscopy in the
renal tubular epithelium of seven of 26
patients with COVID-19 at autopsy.
Electron micrographs from this au-
topsy confirm this finding and provide
strong evidence for direct infection. The
crown-like morphology is similar to pre-
viously published images, and the viral di-
ameter is within the reported 70–90 mm
size range of SARS-CoV-2.10 The organi-
zation of intracellular viruses into arrays is
suggestive of intracellular manufacture
and assembly. The presence of double-
membrane vesicles with possible viral
assembly near the rough endoplasmic re-
ticulum in this case is analogous to the
proposed mechanism for viral assembly
of SARS-CoV-1.15 Finally, vacuolation of
epithelial cells has been reported after in-
fection with SARS-CoV-1, similar to the
isometric vacuoles in the proximal tu-
bular epithelium in this patient.16 The
isometric vacuoles by light microscopy
correlate with double-membrane vesi-
cles containing vacuoles by electron mi-
croscopy and were also noted in a recent
autopsy series.14 Isometric vacuoliza-
tion may be a helpful diagnostic clue
for the presence of direct renal infection,
but this association needs to be con-
firmed in a larger series using immuno-
histochemistry or electron microscopy.
There are notable caveats to the find-
ings in this case report. First, although

A B

Figure 2. Proximal tubular isometric vacuolization by light microscopy correlates with SARS-CoV-2 infection. (A) Toluidine blue–stained
epoxy section with extensive isometric vacuolization of proximal tubular epithelial cells, corresponding to location of intracellular virus by
electron microscopy. (B) Tubular epithelial cells from a section showing mild autolysis and no vacuolization. Electron microscopy showed
no virus present in this section. Both images at 3400 magnification.

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 RAPID COMMUNICATION www.jasn.org

A B
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2 µm 500 nm

C D

200 nm 400 nm

Figure 3. Ultrastructural features of coronavirus infection and replication in proximal tubular epithelial cells detected after death from
COVID-19. (A) Proximal tubule oriented with basement membrane at the bottom and lumen at the top, containing vacuolated and partially
degenerated epithelial cells with abundant viral particles (arrow). (B) Intracytoplasmic viral arrays (arrows) within tubular epithelial cells.
(C) Detail of viruses showing envelope with crown-like projections. Inset: single virus. (D) Vacuole with double-membrane vesicles
(solid arrow) adjacent to ribosome-studded rough endoplasmic reticulum (open arrows), similar to structures reported in SARS-CoV-
1–infected cells.

this renal tissue showed only mild post-
mortem change by light microscopy,
there is still significant ultrastructural
injury. Disrupted plasma membrane-
bound organelles could mimic viral
structures. Second, direct kidney infec-
tion may be an uncommon occurrence
in patients with COVID-19 and renal
dysfunction. Indeed, there was no detec-
tible intrarenal virus by electron micros-
copy in one additional autopsy of a
patient with COVID-19, although that
patient had nonoliguric stage 2 AKI
and interpretation was limited by exten-
sive autolysis. Most importantly, the
identification of direct infection by
SARS-CoV-2 does not preclude other
mechanisms of renal injury in COVID-
19. In this case, coronavirus was only
identified in a subset of tubules, and di-
rect infection is likely either an incidental
finding or a contributing cause of kid-
ney injury. This patient’s renal failure
was likely multifactorial, with preexisting
ischemic renal injury complicated by
progressive hypoxemia and focal viral
infection.
This autopsy report is illustrative of
the increased morbidity and mortality
associated with renal failure and
COVID-19. Additional studies are
needed to determine the frequency of di-
rect renal infection in patients with
COVID-19, and whether there is an as-
sociation with viral titers in plasma or
with preexisting renal comorbidities.
ACKNOWLEDGMENTS
The authors are indebted to Yoel Bailey and
Yinru Sieracki for their invaluable technical
assistance with the electron microscopy, as
well as to Monique Micallef and Lisa Neal for
their expert assistance with the autopsy. Dr.
Jeffrey Myers assisted with evaluation of the
lung pathology.
Dr. Allecia M. Wilson and Dr. Jeffrey
M. Jentzen performed/supervised the au-
topsy. Dr. Evan A. Farkash supervised the
electron microscopy and drafted and revised
the manuscript. All authors approved the fi-
nal version of the manuscript.
Dr. Evan A. Farkash reports personal fees
from Novartis, outside the submitted work.
DISCLOSURES
All authors have nothing to disclose.
FUNDING
None.
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