Life after COVID-19 is now starting to return to normal and the recent EuFMD OS-22 (https://www.eufmd.info/os22) and the Annual Meeting of the WOAH/FAO FMD Network provided welcome opportunities to finally meet colleagues in a face-to-face format after two years of virtual communication. These meetings reviewed global FMD events that include:

1. circulation of a new clade within O/ME-SA/PanAsia-2ANT-10 in Eastern Mediterranean countries. These FMD viruses appear to have supplanted O/ME-SA/PanAsia-2QOM-15 viruses that were previously dominant in this region. [NB: New FMD cases due to serotype O have been reported to WOAH (Israel in September, and Palestine in November and December)].
2. incursions of the O/ME-SA/Ind-2001e lineage into Indonesia, where the WRLFMD has recently co-authored a paper to describe the genome of the FMDV responsible (see:  https://doi.org/10.1128/mra.01081-22).
3. emergence of a new lineage called O/ME-SA/SA-2018 from South Asia into the Gulf States. In India, this lineage is now responsible for approx. 40 percent of serotype O cases and new sequence data analysed in this report demonstrate that the lineage is present in Bangladesh.
4. reports of FMD cases in Egypt with a South American origin. These unexpected outbreaks need to be monitored closely since there is potential for onward spread of these viruses into other countries in North Africa and the Eastern Mediterranean. A shipment of samples from Egypt was received to WRLFMD at the end of the year (results to be reported in Q1 2023).

During this period, the WRLFMD has reported test results for samples received from Sudan and there have also been new sequence submissions from Bangladesh, Israel (KVI), Malaysia (MNFMDL), Mongolia (ARRIAH/GenBank) and Turkey (FMDI). Individual laboratory reports can be retrieved from http://www.wrlfmd.org/ and further information is provided in this report.

During the past three months, the WRLFMD has reported test results for samples received from Ethiopia, Indonesia, Israel, Mongolia, Palestine, Thailand, UAE. There have also been sequence submissions from Botswana (BVI), Egypt (from GenBank), Ghana (NCFAD), Indonesia (Pusvetma), Niger (LABOCEL & ANSES) and Zimbabwe (BVI).

Following on from a peer-reviewed paper describing a serotype O virus of South America origin in Egypt that was published earlier in the year, another paper from a different Egyptian group (https://pubmed.ncbi.nlm.nih.gov/36209919/) has recently reported serotype A viruses from the A/EURO-SA topotype in the country. These unexpected events represent the introduction of completely new viral lineages into North Africa and raise many questions regarding the routes by which these viruses have transited from South America, as well as the potential for these lineages to become established and spread in the region. Elsewhere in Africa, outbreaks due to serotype SAT 2 have occurred within a disease control zone in Botswana, where sequences shared by BVI, Botswana show closest relationship to FMD viruses previously collected across the border in Zimbabwe. In South Africa, new FMD outbreaks due to serotypes SAT 2 (KwaZulu-Natal and Free State) and SAT 3 (Free-state, Gauteng, Mpumalanga, and North-West Provinces) have been reported. FMD cases also continue to be reported in Indonesia and WRLFMD has received representative samples from representative cases (caused by the O/ME-SA/Ind-2001e lineage), where vaccine matching data described in this report provides reassurance about the use of certain FMD vaccines to control these outbreaks.

Further published information including the individual laboratory reports from WRLFMD can be retrieved from the following website (http://www.wrlfmd.org/).

During the past three months, the WRLFMD has reported test results for samples received from Algeria, Botswana, Israel, Malawi, Namibia, State of Palestine, Tunisia, United Arab Emirates and Zambia. There have also been sequence submissions from Indonesia (Pusvetma), Malawi (BVI), Malaysia (MNFMDL), Mali (ANSES), Mozambique (BVI) and Thailand (Pakchong).

During this busy period, greatest attention has been placed on the further expansion of the O/ME-SA/Ind-2001e lineage in Indonesia which had previously maintained an FMD-free status (without vaccination) since 1990. FMD has spread very rapidly and there are now official reports of outbreaks on four main islands (Sumatra, Java, Kalimantan, and Lombok) as well on the Island of Bali (via media sources). Analyses of sequence data reveals a close genetic relationship to FMD viruses collected in Thailand and Malaysia during 2021 and 2022; findings which may help to understand the origin of this incursion. During this quarter, further outbreaks due to the O/EA-3 topotype have been characterised in Algeria, which in addition to earlier cases in Tunisia, pose immediate threats to countries in southern Europe. In southern Africa, the O/EA-2 topotype has continued to spread into new locations (Malawi and Mozambique). In the Middle East a new virus lineage (called O/ME-SA/SA-2018) previously detected in India and Sri Lanka has been detected for the first time (in UAE). Elsewhere, a recent peer-reviewed paper from Egyptian scientists has provided evidence that viruses from the O/EURO-SA topotype are circulating in the country (see: https://pubmed.ncbi.nlm.nih.gov/35679058/). This report has not been officially confirmed, but if true would represent the introduction of a completely new viral lineage with a South American origin into North Africa. 

During this period, the WRLFMD has reported test results for samples received from DR Congo, Jordan, Nepal, Nigeria, Pakistan and Uganda. New data has also been analysed for sequence submissions from Israel (KVI), Namibia (BVI), Kazakhstan & Russia (ARRIAH) and Tunisia (IRVT and ANSES).

Sequences for the FMD viruses causing Russian and Kazakh outbreaks represent further spread of the O/ME-SA/Ind-2001e lineage, where their close relationship to Mongolian sequences highlights the new threats posed by pathway from East to Central Asia (previously last exploited by serotype A viruses in 2013). New cases of FMD in Israel have been caused by viruses from the O/ME-SA/PanAsia-2^ANT-10 sub-lineage most closely related to viruses previous collected in Jordan and Palestine. These viruses also share a common genetic history with FMDVs collected recently from Pakistan (see this report). Elsewhere, sequence data for FMDV-positive samples collected recently from Tunisia shared close relationship to O/EA-3 FMD viruses collected in Nigeria (in 2021), supporting the idea that these cases represent a new introduction of FMDV into North Africa, presumably following a similar trans-Saharan pathway as occurred previously for O/EA-3 (in 2018) and A/AFRICA/G-IV (in 2017).

Regional road map meetings provide a great opportunity to exchange the latest FMD information and Dr Donald King of the WRLFMD was pleased to join two recent meetings in virtual format for East Africa and Southeast Asia.

STOP PRESS

A new FMDV VP1 sequence has been shared by BVI, Botswana for a sample collected in the Central Region of Malawi during February 2022.  This sequence shares closest genetic relationship (>99.5% nt identity) to an FMDV isolate collected in Zambia (in 2018) and demonstrates that the O/EA-2 topotype is now present in Malawi (further details will be presented in the next report). A recent joint paper describes the detection of this topotype for the first time in Namibia.

During this reporting period, results have been reported for samples collected from Iran, Kenya, Mongolia, Nepal, Nigeria and Uganda. Sequence data has also been shared for phylogenetic analyses from Cambodia (via APQA, South Korea), Jordan (via Jordan University of Science and Technology), Nigeria (via NCFAD-CFIA, Canada and NVRI, Nigeria) and Palestine (via KVI, Israel and the Palestinian Veterinary Authorities). Further details of these laboratory results can be retrieved from http://www.wrlfmd.org.

During December 2021, there has been particular focus on FMD outbreaks occurring in the Eastern Mediterranean where FMD cases in Jordan and Palestine have been caused by viruses from the O/ME-SA/PanAsia-2^ANT-10 sub-lineage. These viruses are most closely related to FMD viruses recovered from Pakistan (in 2019), which is perhaps unexpected and poses new questions about the East-to-West connectivity within Pool 3. A contemporary FMDV sequence from the Gaza Strip, Palestine also shows that FMD viruses from the O/EA-3 topotype most closely related to Egyptian FMD viruses (from 2017) are present. Elsewhere, new FMD outbreaks have been recently reported in the Orenburg Oblast in the Russian Federation (in one of the Southern FMD-free (with vaccination) zones) and China.

STOP PRESS

1. an FMD outbreak has been reported (3^rd January 2022) in Kazakhstan (Previously FMD-free zone without vaccination)
2. an FMD outbreak in Tunisia was reported to the OIE (12^th January 2022), where sequence data shared by Institut de la Recherche Vétérinaire de Tunisie and ANSES France highlights a new incursion of the O/EA-3 topotype into the North African region.

This quarter samples have been tested by the WRLFMD from DR Congo, Iran, Kenya, Mongolia, Vietnam and Zambia. Further details about these laboratory results can be retrieved from http://www.wrlfmd.org.

The circulation of O/ME-SA/Ind-2001e continues to be closely monitored in Asian countries where a new paper documents the retrospective detection of this lineage in Cambodia in 2019 (https://www.frontiersin.org/articles/10.3389/fvets.2021.749966/abstract). Data presented at the SEACFMD national coordinators meetings (https://rr-asia.oie.int/en/events/24th-seacfmd-national-coordinators-meeting/) highlighted the increasing dominance of this lineage across Southeast Asia, and results for samples collected in Mongolia reported here provide further evidence that O/ME-SA/Ind-2001e is becoming established in East Asia.

Elsewhere in Asia, Iran has reported a new genetic clade of A/ASIA/Iran-05^FAR-11 (see sections 4.2 in the 2021 Quarter 3 report) which appears to be poorly matched against FMD vaccines that are used in the region (reported at the recent West EurAsia Roadmap meeting by the ŞAP FMD Institute, Turkey: https://rr-europe.oie.int/en/our-missions/animal-diseases/foot-and-mouth-disease/west-eurasia-fmd-roadmaps/). Vaccine matching for representative viruses is underway at the WRLFMD and results will be reported shortly.

Sequence data has also been submitted for phylogenetic analyses from Namibia and Malawi (via the OIE Reference Laboratory in Botswana) to demonstrate that FMD outbreaks reported in Namibia (during July 2021) are due to the O/EA-2 topotype sharing closest genetic relationship to viruses recovered from Zambia (99.5% nucleotide identity: see Section 4.4 in the 2021 Quarter 3 report). The FMD cases in Namibia represent the first occurrence of serotype O anywhere in Southern Africa since 2000, when viruses of Asian origin (O/ME-SA/PanAsia) caused outbreaks in South Africa. This situation will need close monitoring since serotype O vaccines are not so widely used in Namibia, or in neighbouring countries such as Botswana or Zimbabwe.

During this quarter, reports have been prepared for samples submitted from Bahrain, Cambodia, Israel, Laos, Thailand and Vietnam. In addition, phylogenetic analyses have been undertaken for FMDV sequences submitted from Malaysia. As has been highlighted in previous updates, submissions to the WRLFMD have been severely curtailed during the past twelve months due to COVID-19 restrictions, although new submissions received recently at Pirbright from Democratic Republic of the Congo, Iran, Kenya and Zambia (results to be reported next quarter) provide early indication that these transboundary surveillance activities may be slowly recovering. Elsewhere, data from other partner and affiliate laboratories of the OIE/FAO FMD Laboratory Network (See Figure 4 in the 2021 quarter 2 report) indicates that while there was an overall decrease in samples submissions during 2020, the impacts of COVID-19 have not been equally felt across the different FMD endemic pools. In contrast to the reduction in samples tested for Pools 2, 3, 4 (where the greatest relative reduction in numbers was in Pool 4), sample reports increased in the remaining 4 pools during this twelve-month period.

Sequence data from Malaysia and for Vietnamese samples provides further evidence that the O/ME-SA/Ind-2001e viral lineage is now well established as an endemic lineage in southeast Asia. Elsewhere, during this quarter, FMD outbreaks comprising SAT 1, SAT 2 and SAT 3 have been reported to the OIE. Other FMD outbreaks in southern Africa have been reported in Namibia (historical cases of SAT 2 in 2020) and Malawi (not typed).

Sample submissions to International FMD Reference Laboratories have been impacted by the on-going COVID-19 pandemic: despite these current difficulties, the OIE/FAO FMD Laboratory Network (https://www.foot-and-mouth.org) welcomes countries to submit appropriate clinical samples for laboratory analyses – testing is free-of-charge, for further information or assistance with shipments, please contact donald.king@pirbright.ac.uk.
These data highlight two new events:

1. Samples from Mauritius: In recent years, particular attention has focused on FMD viruses that circulate in Pool 2 (South Asia) and the frequency by which these viruses can seed new outbreaks elsewhere. Previous examples of viruses that have spread from Pool 2 include O/ME-SA/Ind-2001 (d and e sub-lineages) and A/ASIA/G-VII. In the Jan-Mar 2021 report, we describe new sequence data that have been provided by ANSES (France) for samples collected on the Island of Rodriguez in Mauritius during March 2021. Analsyses demonstrate that these new sequences belong to the O/ME-SA/Ind-2001e lineage – however, they appear to be distinct from sequences that were detected in Mauritius during 2016.
2. Samples from Bahrain: FMDV sequence data for the samples collected in Bahrain have been characterised as belonging to two East African viral lineages (O/EA-3 and A/AFRICA/G-I). We understand that these samples are from cattle that have been recently imported from Somalia which explains the unexpected origin of these viruses.

A new review article published by the OIE/FAO FMD Laboratory Network provides an overview of the history of serotype C and evidence that this serotype is no long circulating in susceptible hosts (see: https://academic.oup.com/ve/advance-article/doi/10.1093/ve/veab009/6178807). Now that more than sixteen years have passed since the last serotype C outbreak (in Kenya and Brazil in 2004), this paper also makes recommendations to reduce the possibility that this serotype is reintroduced into the field.

In recent years, particular attention has focused on FMD viruses that circulate in Pool 2 (South Asia) and the frequency by which these viruses can seed new outbreaks elsewhere in Asia. Examples of viruses that have spread from Pool 2 include O/ME-SA/Ind-2001 (d and e sub-lineages) and A/ASIA/G-VII. Earlier in 2020, a new serotype O lineage was described for samples collected in Sri Lanka (see Jan-Mar 2020 report); new data provided from ICAR-DFMD India during the OIE/FAO FMD Laboratory Network meeting provides further evidence that this lineage (tentatively named O/ME-SA/SA-2018) is more widely distributed in South Asian countries. Data in this report also describes new genetic clade within the O/ME-SA/PanAsiaFAR-11 sub-lineage which has been detected in Iran and presents the phylogenetic tree for the new cases due to the O/ME-SA/PanAsiaANT-10 sub-lineage detected in Turkey. Elsewhere, sub-clinical cases (due to SAT 1) have been reported in South Africa.

The WRLFMD has been recently working with EuFMD to develop an open-access interactive FMD dashboard to allow users to interrogate, retrieve and display FMD information (including FMDV genomic data). The scope and functionality of the improved tools implemented during this project will be influenced by your requirements and therefore we are seeking feedback to help us to understand how we should prioritise the design of this system. For those you that are interested, please complete the survey in the link: https://forms.office.com/Pages/ResponsePage.aspx?id=Eh70v1zu20izMQzOHucOut-ijsc2qwZOo151ynO2MwhUN01SUFVROTc3TTRYRklEMTU3WU1FTUsyQy4u

In common with the quarter, samples submitted to the WRLFMD during this reporting period (July to September 2020) remain very low. Although it is perhaps inevitable that the international activities of FMD reference laboratories have been impacted by COVID-19, at Pirbright our experience is that air-freight shipments can still be arranged - if they are carefully planned, in advance! We are very happy to be contacted to help address any problems that scientists are experiencing to send samples to WRLFMD for analyses.

In this quarter, there were results for FMDV-positive samples submitted from Vietnam, where three different serotype O lineages were detected (O/ME-SA/Ind-2001e, O/ME-SA/PanAsia and O/SEA/Mya-98). Sequence data submitted from Turkey (from GenBank) and Zambia (from SSARRL for FMD, Botswana) were also analysed. In addition to three phylogenetic trees that reconstruct the spread of the A/ASIA/G-VII lineage in Turkey during 2015-17, more recent data (received in October from the ŞAP FMD Institute, Ankara) highlights a new introduction of the O/ME-SA/PanAsia-2ANT-10 lineage into the country (for the first time since 2017). Elsewhere, there have been reports to the OIE of outbreaks in South Africa (serotype SAT 2), Libya (serotype A), Rwanda (Kayonza; where serotype SAT 2 has been detected by serology), Mozambique (untyped), and southern Malawi (initially reported as untyped – but now typed as SAT 2 by SSARRL, Botswana). Despite the technical challenges of connecting to virtual platforms (via SKYPE, Zoom etc...), a number of international FMD meetings have been scheduled including the National Coordinators of SEACFMD during July and the SADC FMD Roadmap meeting in November. In December, the Annual meeting of the OIE/FAO FMD Laboratory Network and the Open Session of EuFMD will also be held in a virtual-remote format. Finally, I take this opportunity to let FMD colleagues know that WRLFMD and EuFMD will be running an e-learning training course the covers FMD diagnostics starting in November. This course is designed for personnel working in national FMD laboratories and further details are provided in Annex 4 of WRLFMD July - September 2020 quarterly report.

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Congratulations to Keith Sumption in his new role as the CVO for Food and Agriculture Organization of the United Nations (FAO) – and sincerely hope that he will still be able to dedicate some time to FMD-specific issues!

Over the past few months, we have all had to get used to a different way of working including learning new ways of exchanging information via remote meetings. Don King was pleased to “virtually” join in recent meetings of the South-East Asia and China FMD campaign (SEACFMD) National Coordinators to learn about the FMD situation in Southeast Asia and the inevitable impacts of COVID-19 upon local efforts to control the disease. During the shut-down period, staff from the WRLFMD have been deployed to hospitals to assist in routine COVID-19 RT-PCR testing and have also contributed to work to implement new ELISA tests to measure serological responses of COVID-19 vaccine candidates. Work at Pirbright is now slowly getting back to a new “normal” and we have started to receive overseas samples for testing as well as dispatch sample panels for the proficiency testing exercise.

This quarter there are results for samples that have been received from Pakistan where sequences recovered for the samples from Pakistan (2016, 2017, 2019, 2020) cover the three FMDV serotypes (O, A and Asia 1) that are endemic in the country. For serotype O, more than 50 percent of the sequences (n=19) belonged to the O/ME-SA/Ind-2001 clade; findings which indicate that this lineage has become more widely established in the country (after it was detected for the first time in 2019; see: https://mra.asm.org/content/9/18/e00165-20). Elsewhere, new cases of FMD have been reported in Libya (serotype A) and within the FMD protection zone in South Africa (serotype SAT 2).

The information included in the quarterly report from the WRLFMD (https://www.wrlfmd.org/ref-lab-reports) now complements the EuFMD FAST surveillance report for the European neighbourhood (http://www.fao.org/3/cb0215en/cb0215en.pdf).

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There have been new FMD outbreaks in North Africa (Libya), from where the disease threatens the Maghreb countries; the detection of new serotype O lineages in Pool 2 (Sri Lanka) and the complexities of multiple serotype and topotype co-circulations in Pool 4 (East Africa) that indicate that more frequent and timely virus typing is required. Despite the enhanced surveillance work of the OIE/FAO FMD Laboratory Network there are significant and concerning gaps in submissions from Pool 3 (countries in Middle-East and parts of Central Asia), Pool 5 countries in West Africa (Mali, Chad, Niger) and Pool 1 countries (Myanmar and Cambodia).

There is also concern for the lack of typing of samples from Malawi given the southerly spread of FMDV from Pool 4 into Pool 3 during 2018-19 and potential for involvement with risk populations in southern Africa.

All colleagues are encouraged to assist to increase the submissions from these gap areas.

There are currently no headline events before January 2020. However information on FMD events before Janaury 2020 can be found in:

• Annual reports and minutes of the Annual Meeting from the OIE-FAO FMD laboratory network, on this website.
• Quarterly reports from the WRLFMD,found on wrlfmd.org.
• Monthly situation reports from European Commission for the Control of Foot-and-Mouth Disease (EuFMD),found on fao.org.