A Phylogeographic Analysis of Porcine Parvovirus 1 in Africa.

Porcine parvovirus 1 (PPV1) is recognized as a major cause of reproductive failure in pigs, leading to several clinical outcomes globally known as SMEDI. Despite being known since the late 1960s its circulation is still of relevance to swine producers. Additionally, the emergence of variants such as the virulent 27a strain, for which lower protection induced by vaccines has been demonstrated, is of increasing concern. Even though constant monitoring of PPV1 using molecular epidemiological approaches is of pivotal importance, viral sequence data are scarce especially in low-income countries. To fill this gap, a collection of 71 partial VP2 sequences originating from eight African countries (Burkina Faso, Côte d'Ivoire, Kenya, Mozambique, Namibia, Nigeria, Senegal, and Tanzania) during the period 2011-2021 were analyzed within the context of global PPV1 variability. The observed pattern largely reflected what has been observed in high-income regions, i.e., 27a-like strains were more frequently detected than less virulent NADL-8-like strains. A phylogeographic analysis supported this observation, highlighting that the African scenario has been largely shaped by multiple PPV1 importation events from other continents, especially Europe and Asia. The existence of such an international movement coupled with the circulation of potential vaccine-escape variants requires the careful evaluation of the control strategies to prevent new strain introduction and persistence.

Detection and genetic diversity of Mopeia virus in Mastomys natalensis from different habitats in the Limpopo National Park, Mozambique.

Mammarenaviruses have been a growing concern for public health in Africa since the 1970s when Lassa virus cases in humans were first described in west Africa. In southern Africa, a single outbreak of Lujo virus was reported to date in South Africa in 2008 with a case fatality rate of 80%. The natural reservoir of Lassa virus is Mastomys natalensis while for the Lujo virus the natural host has yet to be identified. Mopeia virus was described for the first time in M. natalensis in the central Mozambique in 1977 but few studies have been conducted in the region. In this study, rodents were trapped between March and November 2019in villages, croplands fields and mopane woodland forest. The aim was to assess the potential circulation and to evaluate the genetic diversity of mammarenaviruses in M. natalensis trapped in the Limpopo National Park and its buffer zone in Massingir district, Mozambique. A total of 534 M. natalensis were screened by RT-PCR and the overall proportion of positive individuals was 16.9%. No significant differences were detected between the sampled habitats (χ2 = 0.018; DF = 1; p = 0.893). The Mopeia virus (bootstrap value 91%) was the Mammarenavirus circulating in the study area sites, forming a specific sub-clade with eight different sub-clusters. We concluded that Mopeia virus circulates in all habitats investigated and it forms a different sub-clade to the one reported in central Mozambique in 1977.

Identification of porcine circovirus-3 in Mozambique.

Porcine circovirus 3 (PCV-3) has been associated with an assortment of clinical conditions in pigs and has been reported in many countries worldwide. In Africa there is no data on the presence of PCV-3. In this study, DNA samples collected from 91 pigs between 2011 and 2019 in nine of the ten provinces of Mozambique in the context of African swine fever (ASF) monitoring were further screened for the presence of PCV-3. Of these samples, 7 (7.5%) animals were positive for PCV-3. Sequence and phylogenetic analysis of the capsid protein gene (ORF2) of the PCV-3s provided evidence of epidemiological links with PCV-3s identified in North and South America, Asia, and Europe. This is the first identification of PCV-3 in Mozambique (and Africa) and the first evidence of co-infection of PCV-3 and ASF virus. It should provide a starting point for further investigations into the presence and impact of PCV-3 in Africa.

Porcine circovirus-2 in Africa: Identification of continent-specific clusters and evidence of independent viral introductions from Europe, North America and Asia.

Porcine circovirus-2 (PCV-2) is associated with several disease syndromes in domestic pigs that have a significant impact on global pig production and health. Currently, little is known about the status of PCV-2 in Africa. In this study, a total of 408 archived DNA samples collected from pigs in Burkina Faso, Cameroon, Cape Verde, Ethiopia, the Democratic Republic of the Congo, Mozambique, Nigeria, Senegal, Tanzania and Zambia between 2000 and 2018 were screened by PCR for the presence of PCV-2. Positive amplicons of the gene encoding the viral capsid protein (ORF2) were sequenced to determine the genotypes circulating in each country. Four of the nine currently known genotypes of PCV-2 were identified (i.e. PCV-2a, PCV-2b, PCV-2d and PCV-2 g) with more than one genotype being identified in Burkina Faso, Ethiopia, Nigeria, Mozambique, Senegal and Zambia. Additionally, a phylogeographic analysis which included 38 additional ORF2 gene sequences of PCV-2s previously identified in Mozambique, Namibia and South Africa from 2014 to 2016 and 2019 to 2020 and available in public databases, demonstrated the existence of several African-specific clusters and estimated the approximate time of introduction of PCV-2s into Africa from other continents. This is the first in-depth study of PCV-2 in Africa and it has important implications for pig production at both the small-holder and commercial farm level on the continent.

Prevalence and genome characterization of porcine rotavirus A in southern Mozambique.

Rotavirus A (RVA) is an important pathogen causing gastroenteritis in many species, including humans and pigs. The objective of this study was to determine the prevalence of RVA in pigs from smallholdings and commercial farms in southern Mozambique and characterize the complete genomes of selected strains. RVA was detected at a rate of 11.8% (n = 288), of which 7.6% was detected at commercial farms and 4.2% at smallholdings. The whole genomes of eight rotavirus strains were determined using an Illumina MiSeq platform. Seven displayed a G9P[13] and one a G4P[6] genotype combination, all with a typical porcine backbone (I1/5-R1-C1-M1-A1/8-N1-T1/7-E1-H1). Phylogenetic analysis indicated that the seven G9P[13] strains were in fact one strain that circulated on a commercial pig farm. The genome segments of this strain clustered with diverse segments of human and porcine RVA strains from various Asian countries. Analysis of the G4P[6] strain revealed four distinct genome segments (VP2, VP4, VP6 and VP7) and five genome segments closely related to South African porcine rotavirus strains (NSP1, NSP3, NSP4, NSP5 and VP1). These results suggest that both the G4P[6] and the G9P[13] strains possibly emerged through multiple reassortment events. The presence of these strains on the commercial farms and smallholdings calls for a more in-depth surveillance of rotavirus in Mozambique.

Peste des Petits Ruminants Virus Surveillance in Domestic Small Ruminants, Mozambique (2015 and 2017).

Peste des Petits Ruminants (PPR), a transboundary animal disease affecting mainly goats and sheep is caused by a morbillivirus and threatens food security and livelihoods as morbidity and mortality rates can reach 90%. There are no records of PPR in Mozambique, but the disease situation in Tanzania and the ability of PPR virus to rapidly spread across countries constitute a high risk for about 4.7 million goats and sheep in Mozambique. A total of 4,995 goats and sheep were sampled in several provinces during 2015 and 2017 to assess the status of PPR virus (PPRV) in Mozambique and to contribute to surveillance along the border with Tanzania. The sera were screened for anti-PPRV antibodies using a commercial PPR competition ELISA (c-ELISA) and the haemagglutinin based PPR blocking ELISA (HPPR-bELISA). The swabs were tested using one-step RT-PCR for detection of PPRV RNA. The overall percentage of animals with anti-PPRV antibodies by c-ELISA, was 0.46% [0.30-0.70]. However, all the sera positive on c-ELISA were confirmed to be negative by the HPPR-bELISA. Considering that all the swabs were negative for detection of PPRV, no clinical cases were observed during passive surveillance and active sampling, and no symptoms were reported, these results suggest that PPRV is not present in Mozambique.

Molecular characterization of avipoxviruses circulating in Mozambique, 2016-2018.

Samples from 45 chickens, two turkeys, one peacock and one quail with symptoms of fowlpox were collected in Mozambique between November 2016 and January 2018. Phylogenetic analysis revealed that the samples contained avipoxviruses belonging to both clade A1 and clade A2. In addition, all of the Clade A1 viruses were positive by PCR for the integration of reticuloendotheliosis virus, while the clade A2 avipoxvirus samples were negative. This study confirms the circulation of clade A1 avipoxviruses in Mozambique in addition to identifying clade A2 for the first time in the country.

Detection and phylogenetic characterization of porcine circovirus 2 from pigs in Mozambique.

Porcine circovirus-associated diseases (PCVADs), caused by porcine circovirus 2 (PCV-2), have a significant economic impact on the swine industry worldwide. In Africa, there is little information, to date, regarding the occurrence of PCV-2, and it has not been reported in Mozambique's swine population. We randomly collected mesenteric lymph nodes ( n = 111) from slaughtered pigs from 9 districts in southern Mozambique. PCV-2 DNA was detected in 54% (62 of 111) of the samples and 78% (23 of 31) of the farms. PCV-2 antigen was detected by immunohistochemistry in lymph nodes (6 of 62; 10%) that were positive for PCV-2 by PCR. Histopathologic changes observed in these lymph nodes were lymphoid depletion, multifocal nodal necrosis, and infiltrates of histiocytes and multinucleate giant cells. One positive sample from each district was selected in order to obtain sequences covering the ORF2 region. Five sequences clustered with PCV-2d, of which 3 sequences from Maputo, Namaacha, and Moamba were grouped with PCV-2d-2; 2 sequences from Manhiça and Matola were grouped as PCV-2d-1; and 4 sequences from Boane, Matutuíne, Chibuto, and Xai-Xai were closely related to PCV-2b-1A/B genotypes. Our study indicates that a diversity of PCV-2 viruses is circulating in the Mozambican swine population.

Identification of Clade E Avipoxvirus, Mozambique, 2016.

Analysis of scab samples collected from poultry during outbreaks of fowlpox in Mozambique in 2016 revealed the presence of clade E avipoxviruses. Infected poultry were from flocks that had been vaccinated against fowlpox virus. These findings require urgent reevaluation of the vaccine formula and control strategies in this country.

High seroprevalence of Rift Valley fever phlebovirus in domestic ruminants and African Buffaloes in Mozambique shows need for intensified surveillance.

Introduction: Rift Valley fever (RVF) is an arthropod-borne disease that affects both animals and humans. RVF phlebovirus (RVFPV) is widespread in Africa and Arabian Peninsula. In Mozambique, outbreaks were reported in South; seroprevalence studies performed in livestock and water buffaloes were limited to central and south regions. We evaluated the seroprevalence of RVFPV among domestic ruminants and African buffaloes from 7 of 10 provinces of Mozambique, to understand the distribution of RVFPV and provide data for further RVF control programs. Materials and methods: A total of 1581 blood samples were collected in cattle, 1117 in goats, 85 in sheep and 69 in African buffaloes, between 2013 and 2014, and the obtained sera were analyzed by ELISA. Results and discussion: The overall seroprevalence of RVFPV domestic ruminants and African buffaloes was 25.6%. The highest was observed in cattle (37.3%) and African buffaloes (30.4%), which were higher than in previous studies within Mozambique. In south and central regions, the overall seroprevalences were higher (14.9%-62.4%) than in the north. Conclusion: This study showed the presence of anti-RVFPV antibodies in animals from all sampled provinces, suggesting that RVFPV is actively circulating among domestic ruminants and African buffaloes in Mozambique, therefore surveillance should be intensified.

Phylogenetic analysis of Newcastle disease viruses isolated from commercial poultry in Mozambique (2011-2016).

The complete sequence of the fusion (F) protein gene from 11 Newcastle disease viruses (NDVs) isolated from commercial poultry in Mozambique between 2011 and 2016 has been generated. The F gene cleavage site motif for all 11 isolates was (112)RRRKRF(117) indicating that the viruses are virulent. A phylogenetic analysis using the full F gene sequence revealed that the viruses clustered within genotype VIIh and showed a higher similarity to NDVs from South Africa, China and Southeast Asia than to viruses previously described in Mozambique in 1994, 1995 and 2005. The identification of these new NDVs has important implications for Newcastle disease management and control in Mozambique.

Antibodies against Rift Valley Fever Virus in Cattle, Mozambique

During the past 2 decades, several countries in Africa and the Arabian Peninsula, to which Rift Valley fever virus (RVFV) is endemic, have reported outbreaks of Rift Valley fever in humans and livestock. The first evidence of RVFV in Mozambique was documented as early as the 1960s (1). Endemicity was subsequently confirmed in the 1980s by a prevalence study that identified virusspecific antibodies in 2% of pregnant women (2) and in the 1990s by serosurveillance in Zambezia Province, which showed that cattle had been infected with RVFV.

An investigation into an outbreak of Rift Valley fever on a cattle farm in Bela-Bela, South Africa, in 2008.

In 2008, a suspected outbreak of Rift Valley fever (RVF) was reported on a farm in the Bela-Bela area, Limpopo Province, South Africa. Seven calves died on the affected dairy farm, where no RVF vaccination programme was practised. No apparent clinical disease was reported in the other 300 cattle (33 calves included) or 200 sheep on the farm. During the outbreak, blood samples from 77.7% (233/300) of the cattle and 36.5% (73/200) of the sheep were collected on the affected farm and 55 blood samples were taken from cattle on a neighbouring farm. Eight weeks later, 78% of the cattle (234/300) and 42.5% of the sheep (85/200) were bled on the affected farm only. All sera were tested by an Immunoglobulin M (IgM)-capture Enzymelinked immunosorbent assay (ELISA) and by an indirect Immunoglobulin G (IgG) ELISA. Selected IgM-positive (n = 14), IgG-positive (n = 23) and samples negative for both IgM and IgG-specific antibodies against RVF virus (n = 19) were tested using the serum neutralisation test (SNT). Sera from IgM-positive (n = 14) and negative (n = 20) animals were also tested by a TaqMan polymerase chain reaction (PCR). On the affected farm, 7% (16/233) of the cattle were IgM-positive and 13.7% (32/233) IgG-positive at the first bleed and 2% were IgM-positive at the second bleed, whilst the number of cattle positive for IgG-specific antibodies increased by 21.3% compared with the first bleed. Only 1.4% of sheep were positive for both IgM and IgG antibodies at the first collection; at the second bleed, IgM-positive cases decreased to 1.2%, whilst IgG-positive cases increased to 2.4%. Whilst no IgM-positive cattle were found on the neighbouring farm, 5.5% of cattle were IgG-positive. The SNT confirmed most of the ELISA results, whilst PCR results were all negative. Although serology results indicated virus circulation on both farms, the negative PCR results demonstrated that the animals were not viraemic at the time they were sampled. The movement of infected mosquito vectors by wind over long distances into a low-lying area that favoured their breeding on the Bela-Bela farm may have led to an outbreak of the disease there, but the reason for the low level of virus circulation amongst susceptible animals remains unclear.

Geographic distribution and prevalence of schistosomiasis and soil-transmitted helminths among schoolchildren in Mozambique.

Schistosomiasis and soil-transmitted helminths (STHs) are most prevalent in developing countries. In Mozambique, the first and only national survey of the distribution and prevalence of schistosomiasis and STHs was conducted in 1952 and 1957. Only occasional surveys in restricted areas have been conducted since the 1950s. The objective of our survey was to update information on the geographic distribution and prevalence of schistosomiasis and STHs in this country. During August 2005-June 2007, the Schistosomiasis and STH Laboratory of National Institutes of Health of the Ministry of Health undertook an epidemiologic survey among schoolchildren. A total of 83,331 persons attending primary schools were sampled. The mean age was 11.36 years (range: 7-22 years). Stool and urine samples were collected and examined by using Kato-Katz and filtration and Ritchie and Willis techniques. Results indicate a widespread occurrence of Schistosoma haematobium (overall prevalence = 47.0%) and STHs (prevalence = 53.5%). Prevalence varied dramatically across the country, with the highest prevalence in districts in northern provinces (Cabo Delgado, Niassa, Nampula, and Zambezia) and in certain provincial capital cities. Districts in the southern region of the country were less affected. Schistosoma mansoni was less common, with prevalence of 1%. We conclude that schistosomiasis and STHs are widely distributed in Mozambique and confirm the need for a national helminth control program.