The n e w e ng l a n d j o u r na l of m e dic i n e

C or r e sp ondence

Autochthonous Japanese Encephalitis with Yellow Fever

Coinfection in Africa
To the Editor: Japanese encephalitis virus and
yellow fever virus are mosquito-borne flaviviruses
that circulate in disjunct geographic areas with
different mosquito vectors. Japanese encephalitis
is endemic to most of Asia and the Western
Pacific, whereas yellow fever occurs in tropical
areas of Africa and South America. Both viruses
lead to a wide spectrum of disease severities that
include asymptomatic infection and mild illness
with influenza-like symptoms. However, severe
yellow fever disease can be fatal in 20 to 60% of
cases,1 whereas symptomatic Japanese encephali-
tis virus can progress to severe encephalitis, with
case fatality rates of up to 30%. Survivors often
have long-term neuropsychological sequelae.2
In March 2016, during the yellow fever out-
break in Angola, a 19-year-old man was admitted
to the Cunene Provincial Hospital with a 5-day
history of fever, headache, and jaundice. The
patient, who survived, worked in the capital city
of Luanda at the onset of disease and had not
traveled abroad. A blood sample was obtained,
and a test for yellow fever virus was positive. The
sample was later processed for high-throughput
RNA sequencing. Because the protocol followed
made use of randomly primed cDNA synthesis, it
provided a comprehensive and quantitative view of
all RNA present in the sample, thus enabling the
characterization of potential coinfecting viruses.3
Surprisingly, de novo assembly of the sample
reads revealed a Japanese encephalitis virus ge-
nome (GenBank accession number, KX945367) in
addition to the expected yellow fever virus ge-
nome (GenBank accession number, KX982182).
Phylogenetic analysis revealed that this Japanese
encephalitis virus variant belongs to genotype III,
clustering closely with variants sampled in Asia
(Fig. 1A, and the Supplementary Appendix, avail-
able with the full text of this letter at NEJM.org).
The yellow fever virus sequence was closely re-
lated to both a sequence from the 1971 yellow
fever virus outbreak in Angola and the recently
reported yellow fever virus sequence detected in
a sample from a Chinese traveler returning from
Angola4 (Fig. 1B).
The likelihood of sample contamination is
small, since neither the Institut Pasteur of Dakar,
Senegal, where the RNA extracted from the sam-
ples in Angola was delivered, nor the laboratory
at the Institut Pasteur, Paris, where the libraries
were constructed and sequenced, has ever had
any material containing Japanese encephalitis
virus. In addition, none of the 15 additional
RNA samples from patients with yellow fever
virus who were treated at the same time pro-
vided sequence reads that corresponded to Japa-
nese encephalitis virus. Leftover sera from the
this weeks letters
1483 Autochthonous Japanese Encephalitis
with Yellow Fever Coinfection in Africa
1485 Changes in Frances Deferral of Blood
Donation by Men Who Have Sex with Men
1486 The Blood Supply and Men Who Have Sex
with Men
1487 Ticagrelor vs. Clopidogrel in Peripheral Artery
Disease
1489 Arrhythmogenic Right Ventricular
Cardiomyopathy
1490 Mechanisms and Management of Obesity

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 The n e w e ng l a n d j o u r na l of m e dic i n e

A Japanese Encephalitis Virus

JF915894/China/2009
100
HM596272/Malaysia/1952 Genotype V
100
KM677246/Singapore/1952
AY184212/Indonesia/1981 Genotype IV
HQ223287/Indonesia/1978
100 Genotype II
AF217620/Australia/1995
100
100 AB981183/Japan/2013
100AB853904/Japan/2010
91 KF667326/Taiwan/2012 Genotype I
96
100 KT229573/China/2010
JN711458/China/2009
67
JX072965/India/2010
KU363309/China/2013
100
JN604986/South/Korea/2006
96 100 KC915016/China/2010 Genotype III
68
KF667314/Taiwan/2010
97
JEV/Angola/2016/Cahama-C17
0.07
100 KF667312/Taiwan/2007
58
KF667313_Taiwan_2008

B Yellow Fever Virus

AY640589/Ghana/1927
100
JX949181/USA/NA
100 West Africa I
AY572535/Gambia/2001
100
100 JX898878/Senegal/2005
YFU54798/Ivory/Coast/1982
100 West Africa II
100
JX898869/Ivory/Coast/1973
JF912181/Brazil/1983
100 South America I
KF907504/Bolivia/2009
100
JF912185/Brazil/1992
100
JF912188/Brazil/2000 South America II
100
KM388816/Venezuela/2010
AY968065/Uganda/1948
100
DQ235229/Ethiopia/1961 Central and East Africa
100
JN620362/Uganda/2010
100
YFV/Angola/2016/Cahama-C17
100
KX268355/China/imported/from/Angola/2016 Angola
0.07 100
AY968064/Angola/1971

Figure 1. Phylogenetic Trees of Representative Full-Length Genomic Sequences for Japanese Encephalitis Virus
and Yellow Fever Virus.
Viruses are identified by GenBank accession number. Also included are the names of the countries in which the
sample was obtained, the isolation date, and the viral genotype. The newly sequenced isolates are in bold, italic
type. All horizontal branch lengths are scaled to the number of nucleotide substitutions per site, and the trees were
rooted at the midpoint for the sake of clarity. Bootstrap values are shown for key nodes. Maximum-likelihood trees
were estimated with the use of IQ-TREE (version 1.4.2).

Angola samples were later extracted at Institut
Pasteur of Dakar, and only sample C17 was
positive for Japanese encephalitis virus RT-qPCR.
We found evidence of locally acquired infec-
tion with Japanese encephalitis virus in Africa in
addition to coinfection with yellow fever virus,
which raises the issue of the risk of circulation
of the Japanese encephalitis virus and human
infection in Africa. Since both the vectors and
suitable hosts (e.g., pigs) for Japanese encephali-

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 Correspondence
tis virus are present in Angola, more studies of
this virus in this locality, including serosurveil-
lance, are needed. Increased levels of population
movement between Asia and Africa may provide
opportunities for pathogens to expand their geo-
graphic range. These data also highlight the
potential usefulness of high-throughput sequenc-
ing, particularly untargeted approaches, for patho-
gen surveillance.5
EtienneSimon-Loriere,Ph.D.
Institut Pasteur
Paris, France
etienne.simon-loriere@pasteur.fr
OusmaneFaye,Ph.D.
Institut Pasteur de Dakar
Dakar, Senegal
MatthieuProt,B.Sc.
IsabelleCasademont,M.Sc.
Institut Pasteur
Paris, France
GamouFall,Ph.D.
Maria D.Fernandez-Garcia,Ph.D.
Moussa M.Diagne,M.Sc.
Institut Pasteur de Dakar
Dakar, Senegal
Jean-MarieKipela,M.P.H.
World Health Organization
Luanda, Angola
Changes in Frances Deferral of Blood Donation by Men
Who Have Sex with Men
To the Editor: Since the advent of AIDS, men
who have sex with men (MSM) have often been
permanently deferred from blood donation in
France and elsewhere.1 Such a ban, which is
more stringent than deferrals for other risk ex-
posures, can be considered to be discriminatory
and often is misunderstood.2
In France, the theoretical risk of transfusion-
transmitted human immunodeficiency virus (HIV)
infection is 1 in 3.0 million donations3 (i.e., one
infection per year). However, the last known
case of transfusion-transmitted HIV infection in
France occurred in 2002.
According to the French national surveillance
system for blood donors, between 2011 and
2015, a total of 108 of the 142 donors (76%) who
were found to be HIV-positive were men. Among
these 108 donors, 82 had data that could be
evaluated (see the Supplementary Appendix, avail-
n engl j med 376;15nejm.org April 13, 2017
The New England Journal of Medicine
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Copyright 2017 Massachusetts Medical Society. All rights reserved.
Ibrahima S.Fall,M.D., Ph.D.
World Health Organization
Bamako, Mali
Edward C.Holmes,Ph.D.
University of Sydney
Sydney, NSW, Australia
AnavajSakuntabhai,M.D., Ph.D.
Institut Pasteur
Paris, France
Amadou A.Sall,Ph.D.
Institut Pasteur de Dakar
Dakar, Senegal
Disclosure forms provided by the authors are available with
the full text of this letter at NEJM.org.
1. Monath TP, Vasconcelos PF. Yellow fever. J Clin Virol 2015;
64:160-73.
2. World Heath Organization. Japanese encephalitis vaccines:
WHO position paper February 2015. Wkly Epidemiol Rec 2015;
90:69-87.
3. Matranga CB, Andersen KG, Winnicki S, et al. Enhanced
methods for unbiased deep sequencing of Lassa and Ebola RNA
viruses from clinical and biological samples. Genome Biol 2014;
15:519.
4. Chen Z, Liu L, Lv Y, et al. A fatal yellow fever virus infection
in China: description and lessons. Emerg Microbes Infect 2016;
5(7):e69.
5. Gardy J, Loman NJ, Rambaut A. Real-time digital pathogen
surveillance the time is now. Genome Biol 2015;16:155.
DOI: 10.1056/NEJMc1701600
able with the full text of this letter at NEJM.org),
and of these men, 49 (60%) reported having had
sex with men. Furthermore, among the 22 HIV
nucleic acidpositive, antibody-negative donors
identified between 2001 and 2015, a total of 20
were men (91%), and 65% of the men who had
data that could be evaluated were MSM. Therefore,
during a period in which a policy of permanent
deferral was in place, some MSM donated blood
very soon after they had been infected with HIV.
A more evidence-based deferral policy may result
not only in an unchanged rate of donations from
persons with HIV infection4 but also in enhanced
donor adherence and ultimately in increased re-
cipient safety.
In 2015, the French Health Ministry held ex-
tensive meetings with stakeholders, including
health regulatory authorities, the French national
blood service (tablissement Franais du Sang),