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UNIVERSITY OF CAPE TOWN DIVISION OF MEDICAL VIROLOGY BI-ANNUAL NEWSLETTER
VIROLOGY MATTERS
FEBRUARY 2019
Photo credit: Robyn Walker
Prof. ANNA-LISE WILLIAMSON awarded SAMRC Gold Medal South African Medical
Research Council Gold medals are awarded annually to established senior scien?sts who have made
seminal scien?fic contribu?ons that have impacted on the health of people, especially those living in
developing countries. Anna-Lise is interna?onally recognised in two major research areas. The first is
vaccinology, with an emphasis on the development of novel vaccines, and the second is in the field of
human papillomavirus (HPV) research.
Anna-Lise holds a South African Research Chairs Ini?a?ve (SARChi) research chair in vaccinology and is
ac?vely training many postgraduate students. Her standing is confirmed by an H-index of 47 on Google
Scholar and her work has been cited >6,500 ?mes. We congratulate Anna-Lise on her excep?onal
achievements!
End Of Year Function
This year’s theme for the Virology End of Year
Func?on was “A Minute To Win It”, inspired by
the successful TV show. Contestants had 30
seconds to compete in a series of challenges. The
winners were the “What has Science Ever Done
for Us” Team from Prof Anna-Lise Williamson’s
research group.
Congratula?ons to the winning team!!!
New Staff and Students
DEAN KAYTON
I am a bioinforma?cian in the HIV Diversity Group, Division of
Medical Virology, University of Cape Town. I am a remote
working techie who enjoys living in fun and adventurous
loca?ons off the beaten track. I am currently residing in Kosi
Bay where I get to do things like watch baby turtles hatching,
go over to Mozambique for a daytrip, and sleep in caves in the
middle of nowhere. During the week I am connected up to
electricity and wifi, eyes glued to a laptop screen all day,
naviga?ng the internet for answers to problems which need
solving. I enjoy programming, data science and sta?s?cs. I am
fascinated by ar?ficial intelligence and machine learning,
something I am geing more and more involved in.
I enjoy that my career skills allow me to interface with
specialists in various different areas and I’m having a lot of fun
learning things I never knew about biology in my current role.
FAITH OGUNGBE
I am currently a student at Northwestern University in
Evanston, IL, USA geing my Master of Science degree in
Biotechnology. I graduated from Northwestern in 2017 with
my Bachelor of Arts degree in Anthropology, concentra?ng on
Human Biology with a minor in Business Ins?tu?ons. I am
currently comple?ng an internship with Dr Jo Ann Passmore’s
group to able to obtain my cer?ficate in Global Health and
Sustainability Biotechnologies for my degree. I have truly
enjoyed my experience in the lab and in Cape Town in general
and am excited to con?nue on with this wonderful learning
experience!
MICAELA LURIE
Micaela Lurie is a Masters student, specialising in Medical
Virology, con?nuing from an Honours degree in Immunology
and Infec?ous Diseases. Her work focuses on Chlamydia.
Outside of her academic career, she loves to travel and explore
new places. She func?ons on coffee and popcorn. A huge dog
lover who would one day love to adopt as many as possible.
Graduates
Dr Harris Onywera’s gradua?on,
surrounded by family and Prof
Anna-Lise Williamson
PhD
Margolin
Masters
- Deelan Doolabh
- Fatuma Guled
- Valerie Masete
Honours
- Bekiswa Abulele
- Kate Bergh
- Micaela Lurie
- Temhlanga
Mndzebele
Daniel Sheward was awarded the 2018 Colin
Kaplan Award for his outstanding work in the field
of HIV pathogenesis. Daniel is the first author of a
manuscript published in the high impact journal,
Host Cell and Microbe (2017 impact factor:
17.872), en?tled “HIV Superinfec?on Drives De
Novo An?body Responses and not Neutraliza?on
Breadth”. The journal focuses broadly on the study
of microbes, with an emphasis on the interface
between the microbe and its host.
D a n i e l p l a y e d a n i n t e g r a l r o l e i n t h e
conceptualiza?on of the study including the
formula?on of the aims and methodology. He was
responsible for the data analysis, prepared all the
visualiza?ons and wrote the original drap(s) of the
manuscript.
The manuscript was well received by reviewers
(see excerpts below):
“This is a very important study that I believe will be
the seminal paper going forward on HIV
superinfec?on as it pertains to induc?on of bnAbs.
The study is technically sound and the study well
carried out.”
“The results obtained are important because they
debunk a 25 year old HIV-1 vaccine strategy to
generate broad and effec?ve an?-viral neutralizing
an?bodies that has repeatedly failed and should be
discarded: sequen?al immuniza?on with randomly
chosen heterologous Env immunogens present on
mature virus par?cles.”
“These are important findings building on
technically sound analyses.”
Dean of the Faculty of Health Sciences
Colin Kaplan Award
DANIEL SHEWARD
At the end of 2018, A/Prof. Wendy Burgers took up her award of a Senior Fellowship from the European
and Developing Countries Clinical Trials Partnership (EDCTP). The project is en?tled CaTCH-22 -
C haracterizing the spectrum of T B and C o-infec?on with H IV - the role of Th 22 cells. It will run for the
next 5 years and is valued at over R8 million. The project seeks to understand the extraordinary
suscep?bility of HIV-infected individuals to developing TB, as well as demonstrate a role for different T
helper cell subsets in TB immune control, knowledge which can feed into the ra?onal design of a vaccine
for TB. In par?cular, the project hopes to characterise Th22 cells in TB immunity, and how these cells are
affected by HIV co-infec?on, HIV treatment and TB treatment.
Wendy says: “My team and I are very excited about this fellowship. Not only does it enable us to
con?nue our research in understanding immunity to TB during HIV co-infec?on, but also work on our
favourite cell subset, Th22 cells, which seem to be a limle unusual and HIV seems to like them a lot! Also,
it is essen?ally a capacity development grant – 2 PhD students, an MSc student and a postdoctoral fellow
will be trained over the course of the grant, while undertaking the research. A new postdoctoral fellow
and a Junior Research Fellow will join our team soon, and we look forward to discovering new things and
sharing our findings with the Division. Also to add - these are excellent grants to apply for, for anyone
doing clinical research, and there are fellowships available at senior and training levels. I have a very good
rela?onship with the EDCTP and regularly review EDCTP grants and fellowships, so have insight into what
they are looking for in their applica?ons. If anyone is interested in applying for these funding schemes, I
am happy to provide assistance and advice.”
A/Prof Wendy Burgers awarded EDCTP grant
HIV R4P Conference 2018
Thank you to Debbie Stewart for launching and compiling the
Virology Mamers newslemer for over 5 years!!
We had quite a con?ngent of the ALW plus group (I
am coun?ng in Gerald and Godfrey as well, they
are premy much honorary members) travelling to
R4P this year. Next to enjoying Madrid and the
great food there, we did some real science
ourselves but most importantly, some networking.
Here for instance we’re hanging with Gerald’s
buddies at the opening recep?on. Oh, one of them
turned out to be a journalist from Uganda who
covers scien?fic topics from Africa, so hopefully I
didn’t embarrass myself too much otherwise you’ll
be reading all about that soon.
Although no major breakthroughs were reported at
this HIVR4P mee?ng, the take-home message from
this conference by the leaders in the HIV-
preven?on field is that a vaccine with efficacy of
60% will be sufficient when combined with non-
vaccine based preven?on methods. This was
emphasized in three different plenary talks from
Linda-Gail Bekker, Anthony Fauci and John
Mascola. Although this sounded academically
convincing and a vaccine efficacy of 60% should be
achievable in the near future, I do wonder how this
would work in reality with (lack of) access and
adherence to non-vaccine based preven?on
methods. This first issue was further emphasized
by at least two other plenary talks in which
Maureen Luba gave the example that in her home
country of Malawi the only method of preven?on…
HIV R4P Conference 2018
Phindile presen?ng her Env
Zera-nanopar?cles.
Mani presen?ng his Env protein
produc?on plavorm in plants.
Opening recepLon
Dinner…
Dessert…
Coffee
Dinner… Most of us had
some nice Spanish food in
this busy restaurant, ranging
from lamb chops to pork ribs
which were washed down
with an excellent Rioja.
Godfrey, ordering a burger,
has clearly gone full-blown
American. No paella this ?me
around but we did gorge
o u r s e l v e s o n t h a t t h e
following day in a ?ny limle
place filled with locals.
Dessert… Aper leading us
wrongly to a bakery first,
Mani found us this great ice-
cream parlour in the centre
of town. The bakery did well
out of this limle detour with
M a n i ( s h a m e - ) b u y i n g
possibly one of the worst
c o o k i e s e v e r m a d e b y
mankind for a premy hepy
fee* as well.
- N o t e v e n t a k i n g i n t o
account the exchange rate.
Coffee… Then we stumbled
on this cool limle coffee place
inside a hotel and I felt right
at home, look at this Delp
Blauw lobby!
RecepLon… Everyone hard at
work networking at the
opening recep?on. Judging by
her face, I think Gerald is
having a hard ?me convincing
the journalist next to him of
his point!
The Symposium was held from the 11
th to 15
th December at the Southern Cape Sun Hotel in Cape Town,
South Africa. One of the aims of the mee?ng was to bring HIV genital microbiome researchers together
with pregnancy and reproduc?ve health microbiome researchers to facilitate discussion and collabora?on
between the two groups whose research areas overlap substan?ally.
At the mee?ng the current understanding of female and male genital tract microbiology and immunology,
including func?onal microbiology and biofilms, was presented and knowledge gaps iden?fied. Poten?al
mechanisms leading to adverse outcomes, and a variety of poten?al preven?on and/or treatment
interven?ons, were presented and discussed. It was clear from the mee?ng that exponen?al progress has
been made in recent years and this will hopefully lead to efficacious public health interven?ons to reduce
the high prevalence of adverse sexual and reproduc?ve health outcomes in women, especially in
resource-poor seings.
A/Prof. Jo-Ann Passmore was Co-Chair of the mee?ng and many researchers from the Division of Virology
amended and presented their work, including Prof. Anna-Lise Williamson, Dr Lindi Masson, Dr Rubina
Bunjun, Lyle Curry, Dr Arghavan Alisoltanidehkordi, Anna Happel, Monalisa Manhanzva, Andrea
Abrahams, Dr Brian Kullin, and Dr Ramla Tanko among others.
Source: hmps://www.keystonesymposia.org/18S
Keystone Symposium
Genital Tract Microbiome in Sexual and Reproductive Health
The conference was held from the 2 nd to the 6 th October 2018 in Sydney, Australia. The aim of the mee?ng
was to provide a plavorm for sharing knowledge and research advances on human papillomavirus in
rela?on to cancer development, detec?on, epidemiology and preven?on. It covered a wide range of topics
including viral replica?on and life cycle, func?ons of oncoproteins, genome and RNA modifica?on and
regula?on, HPV tes?ng methodology and applica?on, pathogenesis, epidemiology, cancer screening and
public health issues. Areas related to cervical, anogenital, oropharyngeal and other cancers possibly
associated with HPV were also discussed. Some sessions also focused on HPV genomics with regards to
classifica?on, proposed new classifica?on and use of metagenomics and high throughput sequencing in
discovery of novel papillomavirus types.
The conference was amended by Prof. Anna-Lise Williamson, Dr Harris Onywera, Ongeziwe Taku and
Alltalents Murahwa.
- Alltalents Murahwa
32nd International Papillomavirus
Conference
Farewells
Bioinforma?cian, Dr Arghavan Alisoltanidehkordi had her
final day with the Masson group aper spending a year
working on cervicovaginal metaproteomics analysis. She has
moved to the University of California in the USA where she
is now working in the cancer and gene?cs field.
Her farewell party was hosted at the Mount Nelson on
January 31
st
- The group is sad to see her go but very
excited for her bright future.
Celia Rademeyer has been part of the
HIV Diversity Group for the last 9 years,
and she lep the group in 2018 to take a
break from science for a year or two.
Presently she is taking a more ac?ve
role in her and her husband’s business,
and she has also taken up teaching
pomery (a long-?me dream of hers).
Her full writeup can be seen in the Aug
2018 edi?on of the Newslemer. Her
formal going away was on the 19
th of
October 2018 at Deer Park Café.
Dr Ziyaad Valley-Omar
“I have been in or around the
Division of Medical Virology
since my honours year in 2002.
Back when the ethidium in our
gels was in black and white and
we made up our own mini prep
reagents (kids don’t know how
good they have it). It has been
an honour to study and work
under the guidance of
researchers that I hold in high
regard, who have facilitated
invaluable networking and research opportuni?es. At the
conclusion of my associa?on with the NICD in November, I
commenced with a medical scien?st posi?on within the Groote
Schuur NHLS ?ssue immunology diagnos?c laboratory where my
primary func?on is to setup high-resolu?on HLA typing
capabili?es by next genera?on sequencing for solid organ and
bone marrow transplant purposes. I am a molecular virologist at
heart (I think that’s a thing) and intend to con?nue virus-related
research efforts within my new posi?on through partnerships
with the Division of Virology. I have not lep and you will s?ll find
me lurking whenever and wherever there is cake.” 16
Marius Tincho
What’s the most interes?ng thing about you that we wouldn’t learn from your CV?
That I like to cook my own food thus I hardly eat out or order takeaways.
What is the funniest thing that has happened to you recently?
It may be the fact that many people assume that I am a Jehovah’s witness, because of the way I carry
myself or behave. Also because they assume that many people coming from Central African regional
countries are ChrisLans.
You’ve been given an elephant. You can’t give it away or sell it. What would you do with it?
An elephant is a very big animal and is an endangered species in many parts of the world. Taking it in
this perspecLve, I would return the animal to its natural habitat and make sure that it is taken care of.
On the other hand, it would be nice to lend the animal to others to transport their goods, or it can render
service to peoples. However, looking at the statement in a philosophical way, it would be a big
responsibility to receive such a massive giO and not be able to give it away or sell it. The elephant here
may symbolise, wealth, intellectual knowledge or any valuable item. Thus, it would be unreasonable not
to share it or give it to someone in need. The world we live today is at the crossroad of many turmoils
and we need to change our way of life and behaviour such that we can live together, share with one
another what we possess or have. It is only by given and sharing, help each other, come in need to
someone that we fulfil our true purpose earth, that we find happiness. Hence, I will celebrate the giO I
receive but sharing it with others and they would benefit from it even if they can possess it.
What would your autobiography be called?
“The journey of my life, the product of my efforts”
A penguin walks through that door right now wearing a sombrero.
What does he say and why is he here?
The penguin to me ”Is there a space for me in your house?”
Why is he here? “My habit has been destroyed and I need to adapt to the new situaLon”.
How would you describe your job to a child?
People are different and the way we act, behave, talk and even the way react to problem and happiness,
and it is the same when we become sick. For more than 30 years, there is a bad small animal, called HIV
that make many people become sick when it gets into their blood. Thanks to the fact that we are all
different, some people do not become sick and they can prevent the animal to destroy their body
because their body produces good soldiers that can help fight the bad animal. But other sick peoples
cannot produce these soldiers and they become very sick. And they can die if they are do not receive their
medicines. So, my work will consist of looking at the different substances which allow some sick peoples
to produce these good soldiers and some other sick peoples cannot produce them. I will also examine the
quanLLes of substances produced by sick peoples with good soldiers and compare them with the
quanLLes produced by sick peoples with weak or no soldiers. I will also examine how these quanLLes are
linked to the producLon of these good soldiers.
Getting to know the Virology
team with 6 quick questions
NaLonwide Danish study finds no
associaLon between measles,
mumps, rubella vaccinaLon and
auLsm
S i n c e t h e p u b l i c a? o n o f t h e
controversial Wakefield ar?cle in 1998
(that was subsequently retracted), the
possible link between measles, mumps,
rubella (MMR) vaccina?on and au?sm
has con?nued to cause concern, despite
10 subsequent observa?onal studies
finding no associa?on between MMR
and au?sm.
On Monday the 5
th of March 2019, a
na?onwide study published in Annals of
Internal Medicine (impact factor 19.4)
has found no increased risk of au?sm in
children who received MMR vaccina?on
in Denmark (adjusted hazard ra?o: 0.93;
95% confidence interval: 0.85 to 1.02).
This is one of the largest studies
conducted to date, including 657,
children born in Denmark over a ten-
year period. This study further validates
the results of another study, including
537,000 children that was conducted in
2002 and published in the New England
Journal of Medicine.
Despite this powerful evidence, it is
likely that vaccina?on hesitancy will
persist as parents con?nue to encounter
claims that vaccines cause au?sm on
social media and elsewhere.
Hviid, Anders et al. “Measles, Mumps, Rubella
Vaccina?on and Au?sm: A Na?onwide Cohort
Study.” Annals of Internal Medicine 2019. DOI:
10.7326/M18-
Hot off the press
(available at Annals.org). The crude effect sizes of sex, birth cohort, other early childhood vaccinations, sibling history of autism, and autism risk score are presented in Tables 2 and 3 of the Supplement (available at Annals.org). The high- est risk for autism was conferred by being a boy (HR, 4.02 [CI, 3.78 to 4.28]), being born in a late birth cohort (2008-2010; HR, 1.34 [CI, 1.18 to 1.52]), having no early childhood vaccinations (HR, 1.17 [CI, 0.98 to 1.38]), and having siblings with autism at study entry (HR, 7.32 [CI, 5.29 to 10.12]). The autism risk score had a modest
spectrum cases only resulted in aHRs of 0.96 (CI, 0. to 1.13) and 0.91 (CI, 0.82 to 1.02), respectively. In an analysis taking the second MMR dose into account, there was no evidence of a dose-response (increase in aHR per dose, 0.90 [CI, 0.85 to 0.95]). Adjustment for the potential confounders as covariates instead of strat- ification of the baseline hazard function did not affect the result (aHR, 0.93 [CI, 0.84 to 1.02]). Replacing the autism risk score with the individual covariates used to estimate it in the above model yielded an aHR of 0. (CI, 0.85 to 1.03).
Figure 2. Cumulative incidences of autism (unadjusted and with 95% CI bands) in 657 461 children born in Denmark between 1 January 1999 and 31 December 2010, by vaccination status and age.
Vaccinated Not vaccinated
0.
1 3 5 7 10 14
0.
1. Cumulative Incidence,
% 1.
2.
2.
Children at risk, n Vaccinated
Not vaccinated
3457
Age, y
654 004
571 550 493 444 391 259 235 016
66 497 36 343 27 392 18 949
37 267
823
Annals.org Annals of Internal Medicine 5
aded from https://annals.org by Univ of Cape Town Libraries user on 03/06/
DISCUSSION We found no support for the hypothesis of in- creased risk for autism after MMR vaccination in a na- tionwide unselected population of Danish children; no support for the hypothesis of MMR vaccination trigger- ing autism in susceptible subgroups characterized by environmental and familial risk factors; and no support
cal power and additional susceptible subgroup and clustering analyses. In a 2014 meta-analysis of MMR vac- cination and autism studies, 2 cohort and 4 case–control studies were identified from Denmark (5), Poland (17), Ja- pan (4, 18), the United Kingdom (19), and the United States (20), with no support for an association—for exam- ple, a pooled odds ratio from cohort studies of 0.84 (CI, 0.70 to 1.01) (2).
Figure 3. Association between measles, mumps, rubella vaccination and autism in subgroups of 657 461 children born in Denmark between 1 January 1999 and 31 December 2010.
Factor Hazard Ratio (95% CI)
Hazard Ratio (95% CI)
Cases, n Unvaccinated Vaccinated
P Value
All children Sex Male Female Birth cohort 1999– 2002– 2005– 2008– DTaP-IPV/Hib No DTaP-IPV/Hib 1 DTaP-IPV/Hib ≥2 DTaP-IPV/Hib Autism risk score group Very low risk Low risk Moderate risk High risk Sibling status at age 1 y No siblings with autism Siblings with autism No siblings Father’s ID missing Time since vaccination First year Second year Third year Fourth year ≥4 years
0.93 (0.85–1.02)
0.97 (0.87–1.08) 0.79 (0.64–0.97)
0.84 (0.73–0.96) 1.04 (0.88–1.24) 1.02 (0.79–1.31) 0.94 (0.63–1.42)
1.09 (0.77–1.56) 0.92 (0.74–1.16) 0.92 (0.82–1.02)
0.93 (0.74–1.16) 0.86 (0.71–1.04) 0.91 (0.78–1.06) 1.06 (0.85–1.32)
0.98 (0.84–1.13) 2.69 (0.58–12.43) 0.89 (0.78–1.01) 0.89 (0.45–1.77)
0.96 (0.77–1.18) 0.88 (0.74–1.04) 0.91 (0.78–1.07) 0.96 (0.83–1.11) 0.94 (0.84–1.04)
525
416 109
260 158 75 32
64 92 369
91 133 206 95
227 5 283 10
NA NA NA NA NA
5992
4844 1148
2614 1937 1152 289
71 524 5397
1296 1637 2106 953
2297 32 3594 69
159 410 574 800 4049
0.
0.
>0.
>0.
>0.
>0.
0.50 0.75 0.93 1.5 2.
Fully adjusted autism hazard ratios comparing children who received measles, mumps, rubella vaccine with those who did not. The hazard ratios are depicted on a logarithmic scale, with bars representing 95% CIs. P values are from a test of homogeneity of effect. DTaP-IPV/Hib = diphtheria, tetanus, acellular pertussis, inactivated poliovirus, and Haemophilus influenzae type b vaccine; NA = not applicable.
ORIGINAL RESEARCH Measles, Mumps, Rubella Vaccination and Autism
High impact publications
Page 3
Have you heard?
Addressing vaccinaLon hesitancy through vaccine
communicaLon science
Studies to iden?fy the underlying reasons for vaccina?on failure are
cri?cal for designing vaccina?on interven?ons and campaigns to
increase uptake. A recent study used behaviour–disease interac?on
models to study how vaccine compliance can be influenced by a
wide range of factors.
1 Influen?al factors include lack of disease
awareness and misalignment between individual interest and the
popula?on interest. Another key factor is that vaccines are
imperfect in the sense that (i) there can exist unwanted, adverse
side effects of various degrees, albeit being minor most of the ?me,
and (ii) some vaccines only confer par?al protec?on against the
disease. These factors cause exaggerated perceived risk or cost of
vaccina?on compared to benefit.
In this study, the authors suggest that well-studied mechanisms for
promo?ng altruis?c behaviour can be used to improve vaccine
compliance.
1 Another study published in Nature reported that while
tradi?onal vaccina?on campaigns endorse harm and fairness,
individuals with high levels of vaccine hesitancy value liberty and
purity more highly than those with low hesitancy.
2 Inclusion of
these themes in vaccine discussions may improve coverage.
1 Chen, Xingru, and Feng Fu. "Imperfect vaccine and hysteresis." Proceedings of
the Royal Society B 286.1894 (2019): 20182406. 2 Amin, Avnika B., et al. "Associa?on of moral values with vaccine hesitancy."
Nature Human Behaviour 1.12 (2017): 873.
Precision CRISPR ediLng
The most popular gene-edi?ng tool, CRISPR-Cas9, generates breaks
in the genome that are subsequently repaired by a mix of cellular
pathways. Yet, the repair outcomes are not random. Using
machine-learning algorithms to analyze large amounts of Cas9-
mediated, genome-wide edi?ng events in a range of cells, Shen et
al. , Allen et al. , and Chakrabar? et al. uncovered sequence
determinants of repair outcomes and devised rules to predict
edi?ng products. These findings provide insights into the repair
process and instruct the design of guide RNAs to achieve more
precise edi?ng.
Mao, Steve. "Precision CRISPR edi?ng." Science 363.6424 (2019): 242-243.
