Shedding of Marburg Virus in Naturally Infected Egyptian Rousette Bats, South Africa, 2017

We detected Marburg virus RNA in rectal swab samples from Egyptian rousette bats in South Africa in 2017. This finding signifies that fecal contamination of natural bat habitats is a potential source of infection for humans. Identified genetic sequences are closely related to Ravn virus, implying wider distribution of Marburg virus in Africa.

February-November 2017 were all negative. The number of individual positive rectal swab samples ranged from 1 to 3 per positive pool, totaling 11 positive samples. Only 1 oral swab sample pool, from April 2017, yielded a positive qRT-PCR result, containing a single positive oral swab sample (Table 1). Of 600 rectal swab samples collected during 3 nights in April, 9 (1.5%) were positive; of 215 rectal swab samples collected during 2 nights in September, 2 (0.9%) were positive. We found no significant difference between the number of positive rectal swab samples collected in April and the number collected September. The number of positive rectal swab samples differed significantly from the number of positive oral swab samples collected in April (p = 0.02). Attempts to culture marburgvirus from qRT-PCR-positive swab samples were unsuccessful. Identical results from specimens with cycle threshold (C t ) >30 were obtained in other studies (6,13). We obtained sufficient marburgvirus-specific sequence data only from 1 of the 12 individual positive swab samples for phylogenetic analysis: a rectal swab sample, collected from a juvenile female (bat 8095) in September 2017, from which we recovered 79.2% (15.1/19.1 kb) of the genome. We merged sequencing reads from replicate sequencing runs and mapped 2,472 reads to the MARV reference genome. Maximum coverage per base obtained was 291 reads; some regions had no coverage. The average coverage per base across the genome was 18.5 reads (when we included 0 coverage regions), and the average coverage when we excluded 0 coverage regions was 40 reads. We obtained near-complete coding sequences for the viral protein (VP) 35 (972/990 nt; 98.2%) and VP40 (898/912 nt; 98.5%) genes; coverage ranged from 49.7% (VP24) to 89.3% (glycoprotein) in other open reading frames of the genome.
The marburgviruses sequence (strain RSA-2017-bat8095) detected from the rectal swab sample of bat 8095 shared a common ancestor with all other RAVV complete or near-complete genome sequences, including 3 human isolates from Kenya (14), Uganda (15), and the Democratic Republic of Congo (3) and several bat isolates from Uganda (4) (Figure 1). The RSA-2017-bat8095 nt sequence shared ≈77% identity with the MARV SPU191-13bat2764 Mahlapitsi strain (GenBank accession no. MG725616) that was collected and characterized from Matlapitsi Cave 4 years earlier.

Conclusions
The period of the lowest seropositivity in juveniles (April-May) resulting in the highest number of potentially susceptible bats at Matlapitsi Cave was the same as previously identified (13). This finding coincides with demonstrable seroconversions and virus shedding and represents a period of increased exposure. The significantly higher number of marburgvirus-positive rectal than oral swab samples we detected contrasts with results from experimentally infected Egyptian rousette bats and field studies in Uganda (4,8,9). Experimental data on marburgvirus shedding were obtained from subcutaneously inoculated and colonized Egyptian rousette bats (7)(8)(9). Whether this mode of infection represents a natural portal of entry for marburgviruses in Egyptian rousette bats and to what extent viral shedding patterns in colonized bats can be extrapolated to natural settings are unknown.
Emerging Infectious Diseases • www.cdc.gov/eid • Vol. 26, No. 12, December 2020  Our findings highlight the risk for marburgvirus fecal environmental contamination and for Egyptian rousette bat roosting sites as a possible source of virus spillover. Roosting behavior enabling direct physical contact suggests that fecaloral transmission of marburgviruses in bats can occur. Biting among animals or biting by hematophagous ectoparasites might result in inoculation of wounds with contaminated feces or exposure to contaminated fomites.
Our findings, combined with earlier detection of an Ozolin-like MARV in Egyptian rousette bats roosting at Matlapitsi Cave (13), suggest local co-circulation of multiple marburgviruses genetic variants. Detection of RAVV in South Africa, closely related to East African isolates, indicates that long-distance movement of Egyptian rousette bats contributes to widespread geographic dispersion of marburgviruses. Moreover, it implies that more virulent strains, such as the MARV Angolan strain (2), might be co-circulating. Entering caves and mining have been associated with MARV spillover (3)(4)(5)(6)14,15) and detection of viral RNA in rectal swab samples, highlight the potential route of transmission. Confirmation of the period for the highest virus exposure risk further highlights the value of biosurveillance and demonstrates that marburgviruses continue endemic circulation in South Africa. This circulation represents a potential threat that needs to be communicated to at-risk communities as a part of evidence-based public health education and prevention of pathogen spillover.