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Perspective
Toward a global virus genomic
surveillance network
Verity Hill,1,* George Githinji,2,3 Chantal B.F. Vogels,1,4 Ana I. Bento,5,6 Chrispin Chaguza,1,4 Christine V.F. Carrington,7
and Nathan D. Grubaugh1,4,8,9,*
1Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
2KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
3Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
4Yale Institute for Global Health, Yale University, New Haven, CT, USA
5Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, IN, USA
6The Rockefeller Foundation, New York, NY, USA
7Department of Preclinical Sciences, The University of the West Indies, St. Augustine Campus, St. Augustine, Trinidad and Tobago
8Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
9Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA

*Correspondence: [email protected] (V.H.), [email protected] (N.D.G.)

https://doi.org/10.1016/j.chom.2023.03.003

SUMMARY

The COVID-19 pandemic galvanized the field of virus genomic surveillance, demonstrating its utility for public
health. Now, we must harness the momentum that led to increased infrastructure, training, and political will to
build a sustainable global genomic surveillance network for other epidemic and endemic viruses. We suggest
a generalizable modular sequencing framework wherein users can easily switch between virus targets to
maximize cost-effectiveness and maintain readiness for new threats. We also highlight challenges associ-
ated with genomic surveillance and when global inequalities persist. We propose solutions to mitigate
some of these issues, including training and multilateral partnerships. Exploring alternatives to clinical
sequencing can also reduce the cost of surveillance programs. Finally, we discuss how establishing genomic
surveillance would aid control programs and potentially provide a warning system for outbreaks, using a
global respiratory virus (RSV), an arbovirus (dengue virus), and a regional zoonotic virus (Lassa virus) as ex-
amples.

INTRODUCTION opment of globally adopted genotype and lineage classification

systems would standardize the viral nomenclature and enhance
Virus evolution and genetic diversity can impact outbreak dy- the usability and comparability of the data, and developing better
namics and control efforts. This has been demonstrated to pol- ways of fair data sharing will ensure that they are broadly usable.
iticians, public health professionals, and the public by the Multilateral support from governments, non-governmental orga-
response to the COVID-19 pandemic, in particular with the emer- nizations, and the biotech industry, which all benefit from
gence of variants. Monitoring evolutionary processes can pro- genomic surveillance systems, is required to support these ef-
vide answers that are hidden from traditional epidemiology, forts. Sufficient long-term investment, buy-in, training, and eq-
both on a small scale by investigating the details of transmission uity for genomic surveillance can transform the way our global
chains1 and by uncovering the pathways of spread on a global public health community can respond to both epidemic and
scale.2 Genomic data also has the potential to enhance disease endemic viruses.
forecasting models3 and has been critical for development of
vaccines, therapeutics, and molecular diagnostic assays.4,5
Overall, virus sequencing can be used to better design, apply, MOVING SEQUENCING INTO PUBLIC HEALTH
and evaluate strategies to mitigate transmission and disease.
We call for global virus genomic surveillance networks to pro- Over the last two decades, the output of virus genomic
vide routine data on viral evolution and lineage transmission dy- sequencing has moved from primarily retrospective research to-
namics during and between outbreaks. These programs do not ward near real-time analyses. While the former established the
need to be built from scratch but should utilize the numerous ad- field and is important in its own right for examining longer-term
vancements in sequencing technology that facilitated initiatives dynamics, real-time analyses provide actionable results for pub-
for influenza virus and HIV, outbreak responses to emerging vi- lic health interventions and a clearer return on investment. This
ruses, and the COVID-19 pandemic. At its core is the implemen- transition to real-time assessments established virus genomic
tation of a nimble and adaptable framework, allowing labs to sequencing as a legitimate tool for public health, moving away
sequence and analyze several different viruses with the same from its perception as academic ‘‘stamp-collecting.’’ These
protocol and quickly respond to emerging threats. Further devel- changes were made possible due to innovations in sequencing,

Cell Host & Microbe 31, June 14, 2023 ª 2023 Elsevier Inc. 861
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Perspective

Figure 1. Timeline of public health emergencies since 2000 and associated technological advances
White boxes indicate the timing of the start of epidemics, either based on when the spillover was inferred to happen, or when epidemics were reported or
declared. Purple boxes indicate technological advancements. Countries are colored based on where the epidemic was first detected.

computational technology, and methodological advancements, rus sequencing has for HIV programs, these advancements
as well as new-found demand for rapid results (Figure 1). helped to facilitate genomic surveillance for other public health
Underlying many of the methodological developments of vi- emergencies.
rus genomic surveillance, as well as much of the physical infra- Following HIV, the first epidemic of the 21st century began in
structure and capacity, is the response to the ongoing HIV November 2002 in rural China. Approximately four months later,
pandemic. Due to its high fatality rate when untreated, lack of the cause was identified as a novel coronavirus (later renamed
a vaccine or cure, and socio-political importance, HIV is a pri- SARS-CoV-1) and the first whole-genome sequences were sub-
ority pathogen across the globe. It also has a relatively complex mitted to GenBank in April 2003.7 As the first next-generation
genome for an RNA virus, with circulating recombinant forms sequencing platform (454’s GS20) was not introduced until
and the ability to evolve resistance to drug treatments. For 2005, rapid sequence generation was not possible, and initial
these reasons, genomic surveillance provides a clear benefit. analysis was performed on 14 SARS-CoV-1 genomes, produced
For example, in Portugal, HIV genomes are sequenced as months after the pandemic began.8 After the pandemic, a study
part of routine clinical care and stored in the HIV drug-resis- based on 61 virus sequences identified mutational signatures
tance database.6 Phylodynamic analysis of these genomes common to different phases of the epidemic to explore evidence
contributed to the success of Portugal’s drug decriminalization of human adaptation.9 Therefore, while the SARS pandemic can
policy along with other harm reduction measures for people be viewed as part of the ‘‘genomic age,’’ genomic analysis
who inject drugs and an antiretroviral therapy campaign in beyond identification was limited and retrospective, largely due
reducing the HIV burden.6 In addition to the critical role that vi- to technological limitations.

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Six years later, further technological development enabled vided the context for these clusters and evidence of a new mode
rapid sequencing during the 2009 H1N1 influenza A pandemic. of transmission.
Genomic analyses elucidated its animal origins while the The 2016 Zika epidemic in the Americas also ushered in new
pandemic was still spreading,10 highlighting the need for human technology to improve the scale of virus genomic surveillance.
and animal influenza surveillance. With endemic viruses that Sequencing total RNA dilutes the viral ‘‘signal,’’ which is espe-
have epidemic potential, the financial and political urgency cially problematic with clinical samples that often have low viral
generated during emergencies must be maintained to monitor loads. A highly multiplexed PCR amplicon approach (described
viral diversity. Systematic genomic surveillance has been imple- in more detail below) was piloted during the EVD epidemic18
mented for influenza A virus, and these data are used by the and fully implemented for Zika virus out of necessity—
World Health Organization (WHO) to predict antigenic evolution sequencing had limited success with other methods.22,23 As
and improve vaccine strain selection.11 Further, by regularly later demonstrated during the COVID-19 pandemic, the real
sequencing human viruses, it is possible to identify and track advantage of the amplicon approach is that it massively scaled
markers which may impact transmissibility and vaccine sequencing due to its high per-sample success rate. Amplicon
effectiveness—for example, in the 2016–2017 influenza sequencing, combined with the portable MinION, facilitated a
season in the Northern Hemisphere, many viruses were detected mobile lab to sequence Zika virus across Brazil.24 These data
with a mutation impacting the effectiveness of egg-based were initially used to disentangle the timings of the origin of the
vaccines.12,13 virus into South America,2 as well as later highlighting the impor-
Genomic surveillance is especially important as part of eradi- tance of northeastern Brazil in seeding multiple locations across
cation or elimination programs. In 2014, a polio emergency was Latin America.22
declared as multiple countries had circulation of wild-type polio- In the time since the West African epidemic, Ebola virus
virus, distinguished from vaccine-derived virus through genomic genomic surveillance has become more commonplace, in
surveillance.14 The difference between these two viruses is particular in the Democratic Republic of the Congo. Almost
important, as optimal control strategies vary in terms of the bal- 800 cases were sequenced at regular intervals during the course
ance between using the injected or oral polio vaccines and are of the 2018–2020 epidemic by the Institut de Recherche
indicative of different failures in the eradication strategy.14 Biomedical in Kinshasa. The team analyzed the sequences
Genomic surveillance also complements traditional clinical polio mostly within a month of sample collection to produce genomic
surveillance that tracks cases of acute flaccid paralysis, which epidemiology situation reports in French and English.25 This
occurs in less than 1% of infected individuals.15 Finally, routine genomic surveillance identified superspreading events con-
sequencing can differentiate between outbreaks caused by nected to clergy and motorbike taxi drivers, and the vaccination
new introductions versus cryptic local transmission, identifying policy was subsequently changed to include these professions
high-risk populations that should be targeted for vaccination.16 as high-risk.25 Importantly, this team sequenced 24% of re-
Real-time genomic surveillance, therefore, is a crucial element corded cases, all conducted in-country along with most of the
of the poliovirus eradication effort. bioinformatic analysis with far less reliance on external collabo-
The 2013–2016 Ebola virus disease epidemic (EVD) in West Af- rators than during the 2013–2016 epidemic. This rapid and
rica marked a watershed moment for near real-time viral systematic sequencing program is built on the experience of pre-
genomic surveillance in public health. A total of 1,610 (5%) vious emergencies, and it represents a significant step forward in
cases were sequenced during the epidemic,17 the largest such the inclusion of genomic surveillance for outbreak response and
dataset until the COVID-19 pandemic. This was in part possible sustainable capacity in viral sequencing.
due to advancements in sequencing technology, most notably
the Oxford Nanopore Technology (ONT) MinION, released in MONUMENTAL SEQUENCING EFFORTS DURING THE
2014. The machine’s small size makes it the perfect tool as COVID-19 PANDEMIC
part of a ‘‘lab-in-a-suitcase’’, able to be transported on a com-
mercial flight.18 The MinION also does not require a continuous The sequencing effort during the COVID-19 pandemic is unprec-
mains-power supply and can be run off a laptop battery, edented, both in terms of the number of cases sequenced (over
enabling it to be used in contexts with unreliable power supplies. 14 million) and the number of countries producing their own
While most of the sequences in this Ebola virus dataset were not genomic data26,27 (Figure S1). Within two months of the first
produced with an ONT platform, this represented a major devel- SARS-CoV-2 sequence being released by China Centers for Dis-
opment in the democratization of sequencing and increased the ease Control and Prevention (CDC) on January 11th, 2020,28 25
speed with which future epidemics could be analyzed.19 During additional countries had submitted at least one sequence to the
the epidemic, virus sequencing was used in part to identify sex- data repository GISAID. While some countries were prepared to
ual transmission of Ebola virus in two clusters.20,21 Both clusters sequence a novel virus, many leveraged the urgency of the
were small flare-ups after transmission in the area had ceased pandemic to rapidly build capacity, particularly in Africa and
toward the end of the epidemic, and sequencing revealed that the Caribbean. Substantial investment during 2021 enabled the
cases in the cluster were related to each other and did not consti- Africa CDC to set up or support ten African sequencing
tute a new zoonosis. Further, by using the background genomic hubs.29 The impact of this investment is measurable (Figure 2):
surveillance data that had been sampled throughout the in April 2020, 20 of the 55 (36%) African countries had in-country
epidemic, the latter cluster was shown to be most closely related SARS-CoV-2 sequencing capacity, and by mid-2022, this num-
to a lineage last sampled two years previously, indicating viral la- ber had increased to 39 (71%); and both the volume of se-
tency.21 Thus, genomic surveillance of the whole epidemic pro- quences and the turnaround time substantially improved

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A B

Figure 2. Global SARS-CoV-2 sequencing effort during the COVID-19 pandemic

(A) The number of laboratories worldwide submitting genomes to GISAID, by week and cumulative.
(B) The log number of genomes sampled in each country between 2020 and 2022.

between 2020 and 2021.29,30 A similar trend was observed in grapevine/). The outputs of this pipeline included metadata,
the Caribbean, which had limited local capacity for viral alignments, and a phylogeny, which were then passed to pro-
genomic surveillance prior to the pandemic. In late 2020, ONT grams such as CIVET34 for rapid cluster investigations and close
MinION sequencing was implemented at The University of to real-time phylodynamic analysis and reporting. This had the
the West Indies in Trinidad and Tobago, which provided capa- dual benefit of enabling rapid reporting to governmental funders,
city for 17 member states of the Caribbean Public Health as well as allowing data producers to see real benefit of their
Agency (CARPHA).31 This continued until December 2021, work on a local level in terms of infection control.
when CARPHA developed its own in-house capacity. In addition, A key technological advancement during the SARS-CoV-2
at least 8 of the 30 Caribbean islands now have sequencing ca- pandemic was the development of a lineage classification sys-
pacity and produced their own SARS-CoV-2 sequences. World- tem, providing a relatively universal, high-resolution picture of
wide, by September 2022 over 3,500 labs from 216 countries or the genetic diversity of SARS-CoV-2.35 Along with its associated
territories produced and shared SARS-CoV-2 sequencing data tool (‘‘pangolin’’) to assign those lineages,26 which also has a
(Figures 2A and S1A). user-friendly web browser version (https://pangolin.cog-uk.io/),
While many sequences were generated within the country researchers, clinicians, and policy-makers have a common lan-
from which they were sampled, one of the success stories of guage with which to discuss SARS-CoV-2 genetic diversity in
the COVID-19 pandemic was the development and strength- their region, without having to either generate or interpret phy-
ening of regional sequencing centers. Some, such as the Center logenies. There were also other nomenclature systems devel-
for Epidemic Response and Innovation (CERI) and Kwazulu- oped in 2020, such as the Nextstrain clade system, which aimed
Natal Research Innovation and Sequencing Platform (KRISP) in to describe the phylogeny in a broader and more stable way, by
South Africa, the African Center of Excellence for Genomics of having criteria for minimum size and persistence; as compared
Infectious Diseases (ACEGID) in Nigeria, and Institut Pasteur in to pango lineages which are finer scale to capture outbreaks
Senegal were founded long before the pandemic began. Others, and ongoing transmission in close to real-time.36 However, the
such as the COVID-19 Genomics UK (COG-UK) consortium, clade system became less commonly used as the pandemic
were built rapidly as the pandemic accelerated in 2020. This progressed, and users coalesced more around pango lineages.
speed was possible due to long-standing academic and public In general, having a single nomenclature system in place prior to
health partnerships and decades of previous investment and a major outbreak of a disease, preferably maintained by an inde-
training.32 Clinical and academic laboratories dispersed across pendent organization like the WHO rather than academics,
the UK, which already contained sequencing equipment and would improve communication early on. Along these lines, the
expertise, pivoted rapidly to sequencing SARS-CoV-2. Se- WHO set up a system of naming variants of concern with Greek
quences from the hospital-based and centralized community letters.37 This aimed to make phenotypically important lineages
testing were submitted to the same server, and (along with easier to discuss and to avoid the use of stigmatizing names.
GISAID data) were passed through the same data cleaning and The enormous amount of sequencing data generated during
processing pipeline every day33 (https://github.com/COG-UK/ the pandemic contributed to thousands of high-impact papers

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Figure 3. Modular amplicon-based virus sequencing framework

Steps where swapping of key elements make the framework generalizable to other viruses are highlighted in yellow. Created with BioRender.com.

on national,38 regional,39 and transcontinental virus dynamics Most labs routinely sequencing SARS-CoV-2 include these
and evolution.40 Importantly, this includes the discovery of novel core components (Figure 3).
variants with estimates of their transmissibility and immune
evasion properties.41 It is notable that sequencing efforts (1) Access to remnant diagnostic samples and associated
increased around the time of waves caused by new variants metadata
(Figure 2A; see January 2021 with the rise of Alpha, Beta, and (2) Sample selection
Gamma variants), indicating when it was the easiest to justify (3) Targeted virus amplification or enrichment
the expenditure on genome sequencing. On the flip side, as (4) Preparation of sequence libraries
much of the world is scaling back pandemic control efforts, (5) Sequencing
fewer countries are submitting sequences to GISAID in 2022 (6) Data processing and consensus sequence generation
(Figure S1). Now, the goal globally must be to not lose the finan- (7) Data quality control (QC) checks
cial and training investment developed during the pandemic and (8) Data upload to public databases and storage
to invest some of it into a rapid response system for the next Each step could change when switching to a new virus, but
pandemic, as well as applying it to endemic viruses. some of the most drastic differences are often the protocols to
prepare the samples for sequencing (steps 3 & 4) and the
MODULAR VIRUS SEQUENCING FRAMEWORK downstream data processing (step 6). Most labs sequencing
SARS-CoV-2 (30-kb RNA virus) utilize a highly multiplexed
The new and expanded sequencing capacity implemented in PCR reaction to amplify the virus (step 3), a library preparation
response to the COVID-19 pandemic provides an opportunity optimized for amplicons (step 4), and a bioinformatics pipeline
to create global genomic surveillance systems for other medi- that removes primer sequences and aligns the reads to the
cally important viruses. As the volume of samples needing to SARS-CoV-2 reference genome (step 6). In comparison, the
be sequenced for SARS-CoV-2 declines, those pipelines should standard approach for sequencing human monkeypox virus
be diverted rather than closed—it is much easier to dial complex (200-kb DNA virus) was an untargeted DNA metagenomic pro-
programs up or down rather than on or off. This helps to maintain tocol that sequences most DNA in a sample.42 This approach,
access to diagnostic samples, employment of trained personnel, however, uses completely different reagents and protocols for
equipment functionality, supply stocks, database management, steps 3 and 4, and a different bioinformatic pipeline for step 6,
and, perhaps most importantly, rationale for sustained funding. creating an entry barrier for labs without this expertise. Addition-
Transitioning between different sequencing approaches, how- ally, while metagenomic sequencing is critical for detecting un-
ever, can be harsh. Many SARS-CoV-2 sequencing labs, both known pathogens, it is far less efficient than targeted amplicon
large and small, invested heavily in developing optimal proced- sequencing for viruses. A simpler solution is to adapt the existing
ures and well-trained staff. If the change in approach is major, SARS-CoV-2 pipeline for monkeypox virus, as has been demon-
including needing to purchase new reagents and/or equipment strated with minimal protocol changes.3 By swapping out the
and learn/validate new protocols, the lab may deem the on- PCR primer sets (step 3), the same library prep kits can be
boarding costs too high to justify, and the pipeline turns off. used (step 4) with the lab’s preference for sequencing platform
Thus, the key to diverting sequencing capacity is protocol con- (e.g., ONT, Illumina, Ion Torrent, BGI; step 5). Then the bio-
tinuity. informatic pipelines only need to be updated with the new

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reference files (step 6). This modular approach allows labs to use public health funding follows emergencies, leaving gaps in
a single base set of wet and dry lab protocols for almost any virus routine activities as priorities shift. Continuously restarting tech-
of interest (Figure 3). nical systems like genome sequencing—requiring hiring and/or
Many virus sequencing protocols are already the product of training, purchasing expensive equipment, and validating pipe-
adaptation. The multiplexed PCR-based sequencing approach lines—is an inefficient way to spend money. Rather, long-term
used for SARS-CoV-2 is a derivative of a protocol originally support is needed to maximize the returns. In well-resourced
designed for Zika virus23 and is similar to approaches for countries, the major obstacle is political buy-in. SARS-CoV-2
sequencing Ebola virus and historical HIV samples.18,43 sequencing during the COVID-19 pandemic demonstrated its
These protocols all use dozens, sometimes over a hundred, of value, with even some influential politicians calling for its
overlapping primer pairs to amplify the target genome in two increased usage. The real challenge is convincing leaders of
PCR reactions. A primer design tool called ‘‘PrimalScheme’’ the value of routinely sequencing medically important endemic
(primalscheme.com18,23) makes it easy to design amplicon viruses as a standard component of surveillance, which could
schemes for other viruses—for example, sets for chikungunya, provide the biggest benefit to public health. Not only could it
Yellow fever, and West Nile,44,45 in addition to the widely used enhance forecasting3 and the precision of control methods
SARS-CoV-2 schemes. Many other renditions of the base virus (see Case Studies section below), but it would also create the
amplicon protocol have also been developed,46,47 and primer infrastructure to rapidly and efficiently respond to outbreaks.
schemes are relatively easy to design with adequate genomic in- Thus, we urgently need more studies that highlight the financial
formation. Then, regardless of what amplicon library prep kits or return on investment that routine virus sequencing provides to
sequencing platforms a lab may use, custom or validated primer help justify its permanence in public health.
schemes can be easily exchanged to sequence different viruses. For global virus genomic surveillance systems to be success-
A generalizable modular sequencing approach also simplifies ful, strengthening sustainable efforts in low and middle-income
the bioinformatic pipelines used to process the data. For countries (LMICs) is key. Here, convincing political leaders for
example, software packages like iVar,44 which utilizes standard access to funding may not be the primary barrier if those re-
programs for analyzing sequencing data (e.g., BWA and SAM- sources do not exist. One solution is for new grants focused
tools48,49), are designed for amplicon sequencing pipelines and on long-term programs that encourage local sequencing to be
are virus-agnostic: the user provides the primer scheme genome specifically awarded to principal investigators in LMICs. These
coordinates (i.e., BED file for primer sequence trimming) and the investments, if made to be sustainable, would thereby build ca-
reference genome (i.e. FASTA file for aligning reads to create a pacity and shift leadership opportunities from high income coun-
consensus genome). There are likely magnitudes more custom tries to LMICs. In addition, the biotech industry should directly
bioinformatic pipelines than there are wet lab protocols. The support the system from which they profit. For example, Pfizer
key is to design them to be ‘‘plug and play’’ with validation is predicted to make $34 billion in 2022 from the bivalent
checks to ensure that the pipelines can process different virus COVID-19 vaccine that was only possible through global variant
genome structures (e.g., lengths and segments) and alignment surveillance,52 but the company did not provide any financial
depths. As amplicon-based sequencing data are notoriously support (or bivalent vaccine doses) to South Africa where Omi-
prone to contamination, these modular strategies can also help cron was first identified. Without sustained support, LMICs are
to standardize the quality control steps to ensure accurate forced to find ways to make available resources go further. The
data releases and reporting. modular sequencing framework that we describe above would
Modular protocols can make it feasible and more economical thus be advantageous as the same reagents could be used for
to establish routine sequencing of multiple endemic viruses that many different viruses. Portable sequencers like the ONT
are important to the region. Importantly for when a new virus ar- MinION can also reduce the entry price, and they can be scaled
rives, it also provides the framework to rapidly respond. for bulk sequencing. This also eliminates the annual license and
service costs that come with large benchtop sequencing plat-
OPPORTUNITIES TO OVERCOME EXISTING forms. Finally, smart sampling designs can help to ensure the
CHALLENGES most value per genome, as routinely sequencing a large propor-
tion of the cases (e.g., >10%) may not provide much new infor-
Even with available sequencing tools, establishing virus genomic mation for surveillance.27,53
surveillance networks requires addressing several inequities. Exacerbating the funding issues is that the costs of obtaining
Despite the monumental efforts to sequence >14 million equipment and reagents in many LMICs can be 103 higher
COVID-19 cases, SARS-CoV-2 sequencing was still unbal- than in Europe and North America. Further, significant delays
anced.27 This is because investment in public health is often in customs can lead to reagent degradation,25 and materials
lacking, especially in low-resource settings, where genomic sur- from some vendors are not even possible to obtain (e.g., ONT
veillance efforts compete with the more fundamental needs that in parts of South Asia). We desperately need a call to action to
support testing and medical countermeasures.50 Thus, countries limit price inflation from secondary vendors and expand distribu-
must first and foremost improve their disease surveillance sys- tion centers across the Global South to ensure access to mate-
tems, which would then create the networks and systems to inte- rials at a lower cost. Hopefully, if routine sequencing increases in
grate virus genomics into public health. LMICs, vendors will make a concerted effort to target these
At the forefront of the challenges is funding. Even in well-re- emerging markets for their businesses. These suggestions, how-
sourced countries like the US, public health is woefully under- ever, do not address all of the challenges of balancing genomic
funded despite its significant return on investment.51 Typically, surveillance.

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Access to training programs or a trained workforce can around of sequences into readable reports or dashboards like
impede the establishment of routine sequencing in many envi- Nextstrain,57 allowing local sample collectors to act on their
ronments, but this is an even greater concern in LMICs. In the data where necessary, and to see where their region fits into
wet lab, learning the sequencing protocols is relatively straight- the wider picture. A major drawback of a centralized system is
forward as it mostly uses standard techniques like PCR and pu- a lack of agility: it is much harder to focus on locally important
rification. The main focuses for the wet lab training should be on questions, such as a hospital outbreak, and results can be
workflows and QC to prevent and monitor contamination, proto- slower. Finally, centralization can lead to a lack of local capacity
col troubleshooting, and operating the sequencing platforms. development, possibly focusing human and financial resources
The dry lab is a greater challenge as there are fewer public health on locations or countries that already have better capacity, exac-
professionals with bioinformatics training. It may not be difficult erbating existing inequities. Therefore, the ideal would be a bal-
for someone with basic knowledge of the command line to run ance of centralized and localized capacity to maximize efficiency
a data processing pipeline, but this should not be a ‘‘black without losing the flexibility and speed of small-scale sequencing
box’’ in case of errors or the need to adapt. Having remote col- and maintaining capacity at a local level.
laborators is a temporary but useful solution, especially for skill The above does not solve all of the issues with creating
transfer in the early stages of setting up a genomic surveillance balanced global surveillance systems. The ultimate goal, one
system in LMICs. However, autonomy through local expertise that is easier said than done, is to (re)distribute the resources
is best for the long-term success of a program. Hence, expand- needed for routine sequencing to create an equitable system.
ing training programs like those listed in Table S1 are crucial for As demonstrated by the emergence of SARS-CoV-2 variants, in-
genomic surveillance systems. ternational surveillance is as important for local public health ac-
Centralized sequencing, on a national or regional level, pre- tions as local surveillance.
sents a solution to many of the above issues. Its main advantage
is the focusing of funding; instead of many labs competing for ALTERNATIVE APPROACHES TO SUPPLEMENT
limited resources, larger centers can apply for larger grants CLINICAL SEQUENCING
from international organizations. This greater level of funding
can then translate into several key elements. Higher throughput Routinely sequencing from local outbreaks is not the only way to
sequencing equipment is expensive to buy but is ultimately conduct virus genomic surveillance. Gaps in resources, lab ca-
cheaper per sample,54 making sequencing more cost-effective. pacity, and access to clinical diagnostic samples can delay the
Higher-powered computational equipment means that more implementation and routine availability of bulk sequencing.
complex analyses can be done faster and coherent datasets Thus, it is important to have alternative strategies to supplement
can be generated in real-time, as in COG-UK (see above). Larger, the sequencing of diagnosed cases to still obtain a population-
well-funded centers also attract the top talent in the region, level view of circulating lineages. Moreover, sequencing environ-
focusing expertise in a single area and enabling successful col- mental and (in)vertebrate animal samples can help to reveal
laborations. This expertise can then be used to advocate for a epidemiological patterns that would otherwise be hidden by
region, both geopolitically (as with campaigning for cheaper re- only using human samples. The exact approaches and sample
agents) and in building wider capacity through training. Finally, types rely heavily on the viruses of interest.
the efficiency of sequencing centers carries through into sample International travel surveillance can supplement regional sur-
selection. With a top-down overview, it becomes possible to veillance by essentially using humans as sentinels. It can be
select representative clinical samples based on location and used to sample neighboring countries at border crossings or
time (Box 1 in Hill et al.55), allowing more viral diversity in the re- even the whole world at transport hubs. This is especially impor-
gion to be sampled with fewer resources. tant when the country itself is not willing or able to perform its
There are specific concerns that must be addressed if a own genomic surveillance. For example, diagnostic testing and
centralized model is adopted. First, specimen transport is not sequencing of travelers entering Florida, US, uncovered an unre-
a trivial issue, and networks must be set up to ensure rapid ported Zika outbreak in Cuba in 2017, a year after the epidemic
and safe transport, especially important when dealing with clin- was thought to be over.58 Combined with new phylodynamic
ical samples of high biosafety-level pathogens.25 This may be methods to explicitly include travel data in the reconstruction
mitigated partially by building on existing non-genomic labora- of ancestral node locations,59 this information can be powerful.
tory networks, such as those set up for diagnosing existing Travel sampling can be integrated into existing points of entry
priority pathogens. Connected to this, laboratory information control measures, performed at borders to help prevent the
management systems (LIMS) that keep metadata connected to spread of an infectious disease of interest, and so is relatively
specific samples are integral. Successful LIMS can rely on sim- cost-efficient to set up.55,60 Without local surveillance, however,
ple measures like consistent serial numbers, or more complex simply sampling travelers may only provide a limited picture of
ones including scanning sample barcodes at each stage of its locally circulating lineages and transmission dynamics.
transport. Keeping accurate labels and dates is vital for correct Wastewater genomic surveillance can be useful in monitoring
analysis further downstream, as found when the evolutionary the levels of virus in a given community when a sufficient amount
rate of Ebola virus was underestimated due to taxon label misas- is known about how case counts correspond to the virus con-
signment.56 centration in sewage. It has been used extensively in detecting
Maintaining local ownership of the data (sovereignty) and poliovirus because only 1% of those infected have recognizable
associated buy-in by sample collectors can also be tricky with symptoms. Recently, poliovirus was unexpectedly detected in
a centralized approach. This can be mitigated by the fast turn- wastewater in London, leading to a vaccination campaign in

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young children. After subsequent sequencing, this outbreak was data ownership. The primary challenge is that sequencing data
connected to poliovirus detected in wastewater and New York are highly valuable. They can lead to publications in high impact
City and Israel.61 This approach has been extensively validated journals and reveal information that can negatively impact a na-
for monitoring SARS-CoV-2 transmission and variant detec- tion’s economy. For example, with the SARS-CoV-2 Omicron
tion.62,63 Wastewater sampling is also an avenue for sampling variant discovered in South Africa, and to a lesser extent the
other animal reservoirs of disease, for example, the possibility Alpha variant discovered in the UK, sharing data warned the
of cryptic SARS-CoV-2 lineages originating from rats in the world of the next major COVID-19 wave, but resulting in many
sewers of New York City.64 While the use of wastewater for virus countries instituting severe travel restrictions.71,72 Therefore,
genomic surveillance will likely dramatically rise in years to rapid data sharing needs to be delicately balanced with protec-
come, it is important to highlight that the non-linear relationship tions for the data generators. Some will ultimately choose to not
between clinical cases and the amount of virus in sewage is share their data to ensure protection and sovereignty, but the
pathogen specific and thus not trivial to properly interpret waste- public health benefits will be maximized when everyone has
water data signals. Furthermore, wastewater is not a universal access.
approach as it can only be used to detect viruses that are shed Repositories with fair data usage policies are instrumental in
in urine and/or feces. the success of large-scale genomic surveillance and sharing of
For respiratory viruses, air filter sampling is a new method of information among countries. GISAID emerged as one of the
non-targeted surveillance.65 Like wastewater sampling, viable most important platforms, developed for influenza A virus and
virus can be amplified and then sequenced to examine what is then adding SARS-CoV-2 and now human monkeypox virus.73
present in an area. Further, given that transmission risk is asso- GISAID aims to strike the balance between data protection
ciated with the amount of virus in the air, sampling air filters from and accessibility by requiring user agreements to recognize
public places could help understand the relationships between data producers as authors or in the acknowledgments where
exposures and infections and evaluation control measures necessary. The question of where future data should be stored
(such as mask-wearing). Similar to other indirect forms of surveil- remains open: GISAID has many advantages, but with restric-
lance, the relationship between prevalence and virus nucleic tions on how much data can be downloaded at once, it can be
acid in the air needs to be investigated, the approach validated difficult to use for broad surveillance. Further, it is owned by a pri-
and sampling technology improved; but it remains a promising vate individual, which raises issues for its governance and sus-
avenue for surveillance.66 tainability. NCBI GenBank, run by the US National Institutes of
Genomic surveillance for zoonotic and arthropod-borne vi- Health, is widely used for other virus genomic data, but it has
ruses should also include sampling from their animal reservoirs no protections for data producers. While these and other data
or vectors to better understand the context of outbreaks. Viruses sharing platforms continue to be important for genomic surveil-
like Lassa, Ebola, and monkeypox are primarily maintained in an- lance, new systems developed directly from the input of diverse
imal reservoirs and human outbreaks are the result of spill- stakeholders are still needed.
overs.67–69 Reservoir surveillance and sequencing, when The WHO has recently released a new set of guidelines for
possible, can help detect new spillover or spillback events and pathogen genomic data sharing. They emphasize the impor-
monitor for changes in transmission modalities (see Lassa virus tance of pragmatism in data generation, including that the first
section below). For arthropod-borne viruses, sequencing from sequences from a region have more impact on the dataset
invertebrate vectors is often crucial for revealing ecological fac- than further sequences from a well-represented region, and
tors that drive outbreaks.70 This is especially true for viruses like (sometimes) that speed matters more than absolute correctness.
West Nile (mosquito-borne) and Powassan (tick-borne) in which They also recommend building on the FAIR (findable, accessible,
(1) humans are ‘‘dead-end’’ hosts, (2) human cases are not often interoperable, and reusable) framework to explicitly include eq-
detected, and (3) produce low viremias in humans, making it uity.74,75 These guidelines represent the start of the formalization
nearly impossible to routinely sequence only from clinical sam- of the data sharing discussion, and this must continue to find the
ples. Thus, effective genomic surveillance programs for zoonotic best balance of protection vs usability, how to enforce usage
and arthropod-borne viruses must also establish relationships agreements, and who should host the database itself.
with the groups that are able to routinely sample (in)vertebrate
animals to complement sequencing from human cases. CASE STUDIES
Sequencing viruses from human clinical samples may not al-
ways be the most efficient or informative method for genomic In the following sections, we highlight how enhanced genomic
surveillance. Creative ways to supplement clinical sequencing, surveillance could help the control efforts for different types of
like with travelers, wastewater, or air, are not only critical when endemic viruses: RSV (respiratory, global distribution), dengue
resources are low, they may provide early outbreak signals. virus (mosquito-borne, tropic/subtropic distribution), and Lassa
The key to implementation is partnerships across disciplines. virus (zoonotic, regional distribution in West Africa).

BALANCING DATA SOVEREIGNTY AND SHARING Respiratory syncytial virus

RSV is a leading cause of lower respiratory illness among infants
An effective virus genomic surveillance network requires fair and and children under the age of 5 years,76 especially in LMICs.77
open data sharing within hours to days of generation. This can be Globally, RSV transmission follows seasonal patterns and ex-
complicated by many factors, from technical issues regarding hibits a short doubling time.78 It typically causes over 34 million
the ease of data submissions to more political issues about episodes of acute lower respiratory tract illness per year,77 but

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Perspective

the public health practices implemented during the COVID-19 mosquitoes will have ubiquitous effectiveness. Thus, to monitor
pandemic have significantly disrupted the global RSV dynamics. and help refine these approaches, and provide epidemiological
For example, in the US, there were almost no cases in the winter data on emerging lineages, routine dengue virus genomic sur-
of 2020-21, an out-of-season epidemic in 2021,79 and record veillance is desperately needed.
highs in the fall of 2022. Many pediatric infectious disease wards Using a sample size calculator,53 10,000 dengue virus infec-
are at or exceeding capacity with RSV and other respiratory dis- tions would need to be sequenced per year to detect an
eases, including influenza. emerging lineage in the Americas at 1% frequency with 95%
RSV circulates as RSV-A and RSV-B serotypes which are confidence (assuming equal sampling distribution). From
defined by antigenic and genetic heterogeneity.80 Both RSV-A 2019–2022, that is 40,000 of the 9.1 million (0.4%) dengue
and RSV-B comprise multiple genotypes, 10 for RSV-A and 13 cases reported in the Americas. From that period, only 367
for RSV-B, each of which is characterized by sequential variant sequenced dengue virus genomes (>70% coverage) were
replacement, and which often co-circulate during seasonal epi- deposited in the GenBank data repository. This shortcoming is
demics80 and leads to frequent reinfections.81 Effective specific not entirely due to the COVID-19 pandemic as less than 3,000
treatment for RSV remains a challenge, and several vaccine can- dengue virus genomes have been deposited in GenBank from
didates and monoclonal antibodies are at different stages of the region since 2000. On the other hand, 400,000 COVID-19
development.82 Notably, the bivalent RSV perfusion vaccine by cases have been sequenced in the Americas, demonstrating
Pfizer was reported to be 82% effective in protecting infants in that the infrastructure is currently in place to implement genomic
the first 3 months of life and reportedly effective in preventing surveillance for dengue and other important endemic viruses.
RSV disease during the first six months of life.83 For the vaccines Now is the time to make the coordinated push before the wide-
to have a global impact, however, they need to be fairly priced, spread roll-out of dengue vaccines.
be available in LMICs, and be broadly effective at reducing trans-
mission of the 23 genotypes. Lassa virus
Despite the high disease burden, there are only 2,500 RSV Lassa virus is transmitted by multimammate mice in West Africa
genomes available in GenBank, and none from the case resur- where it can cause acute hemorrhagic fever. While there is no ev-
gence in 2022. The importance of sustained and continuous sur- idence of sustained human-to-human transmission, there was a
veillance cannot be overstated given RSV’s antigenic diversity large uptick in cases in Nigeria in 2018, raising concerns that it
and capacity for rapid genotype turnover. For example, genotype may be spreading between people. Two studies sequenced 50
BA in RSV-B emerged in 1999 and replaced all other RSV-B ge- cases in real-time, which was sufficient to confirm that the uptick
notypes in circulation, potentially through enhanced immune was due to increased spillover from the reservoir and not a change
escape due to a 60-nucleotide duplication in the glycoprotein.84 in transmission route.67,90 While successful in this case, relying on
With the potential for vaccine roll-out in the near future, geno- emergency research instead of routine surveillance is unsustain-
type-level dynamics must be monitored to detect any further im- able and unreliable. Further, the response is slower: the authors
mune escape; and with rapid variant turnover, vaccines may need of the former study were approached at the peak of cases, rather
to be matched to circulating strains, as with influenza. Further, than being able to continuously monitor the situation.
connecting viral genotypes to phenotypes to better predict years Lassa virus is currently only known to be endemic to West Af-
with high RSV circulation or severity would enable pediatric rica, but beyond the obvious moral imperative to prevent disease
healthcare to prepare, as well as raise the index of suspicion for everywhere in the world, there is also a global benefit for estab-
children with respiratory illness. Routine genomic surveillance is lishing sustainable local surveillance programs. A comparison
critical to not only understand the drivers of epidemics, but also can be drawn with human monkeypox virus, which appeared
to help ensure that the new vaccines will be broadly effective. to have stuttering transmission chains in rural West and Central
Africa but found a new niche and is spreading in sexual networks
Dengue virus across the world.91 Local surveillance can detect changes in
Roughly half of the global population is at risk of dengue virus, epidemiology, and therefore a rapid response if transmission be-
causing 100 million symptomatic infections per year.85 In the tween humans becomes more efficient: it is thought that human
Americas, the two highest years on record for reported dengue monkeypox virus was spreading locally between humans for five
cases were 2019 and 2022.86 Dengue virus is endemic to most years before it began to spread globally.92 By implementing local
of the tropical and subtropical regions where its primary mos- genomic surveillance of Lassa virus, significant changes to its
quito vector, Aedes aegypti, resides. With rising global tempera- epidemiology could be detected and contained prior to a global
tures, the habitat for Ae. aegypti is likely to expand.85 New outbreak. This could be built on the existing, strong genomic ca-
dengue control methods, however, provide optimism. Other pacity in Nigeria,90 and Senegal, as well as strengthening the ca-
than Dengvaxia, a vaccine only recommended for those who pacity in Guinea, initially developed during the 2013–2016 EVD
have previously had dengue, there are several promising late- epidemic.93
stage vaccines, as well as many other preclinical and clinical
candidates.87 Programs are also deploying Ae. aegypti mosqui- Conclusion
toes infected with Wolbachia bacteria that, amongst other prop- Genomic surveillance is a crucial tool for public health response
erties, limits dengue virus replication.88 These new control tools to epidemic and endemic viruses. Twenty years of infrastructure
could significantly reduce the future burden of dengue. As building and technical advancements in response to the HIV
dengue virus is genetically diverse both within and between its pandemic and acute emergencies has culminated in a stag-
four serotypes,89 it is not certain that vaccines or modified gering sequencing effort during the COVID-19 pandemic. The

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Perspective

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